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Institute
- Institut für Biochemie und Biologie (26)
- Institut für Geowissenschaften (24)
- Extern (23)
- Institut für Physik und Astronomie (21)
- Institut für Chemie (18)
- Hasso-Plattner-Institut für Digital Engineering GmbH (17)
- Institut für Umweltwissenschaften und Geographie (13)
- Department Sport- und Gesundheitswissenschaften (7)
- Department Psychologie (6)
- Institut für Ernährungswissenschaft (6)
Ribosomes decode mRNA to synthesize proteins. Ribosomes, once considered static, executing machines, are now viewed as dynamic modulators of translation. Increasingly detailed analyses of structural ribosome heterogeneity led to a paradigm shift toward ribosome specialization for selective translation. As sessile organisms, plants cannot escape harmful environments and evolved strategies to withstand. Plant cytosolic ribosomes are in some respects more diverse than those of other metazoans. This diversity may contribute to plant stress acclimation. The goal of this thesis was to determine whether plants use ribosome heterogeneity to regulate protein synthesis through specialized translation. I focused on temperature acclimation, specifically on shifts to low temperatures. During cold acclimation, Arabidopsis ceases growth for seven days while establishing the responses required to resume growth. Earlier results indicate that ribosome biogenesis is essential for cold acclimation. REIL mutants (reil-dkos) lacking a 60S maturation factor do not acclimate successfully and do not resume growth. Using these genotypes, I ascribed cold-induced defects of ribosome biogenesis to the assembly of the polypeptide exit tunnel (PET) by performing spatial statistics of rProtein changes mapped onto the plant 80S structure. I discovered that growth cessation and PET remodeling also occurs in barley, suggesting a general cold response in plants. Cold triggered PET remodeling is consistent with the function of Rei-1, a REIL homolog of yeast, which performs PET quality control. Using seminal data of ribosome specialization, I show that yeast remodels the tRNA entry site of ribosomes upon change of carbon sources and demonstrate that spatially constrained remodeling of ribosomes in metazoans may modulate protein synthesis. I argue that regional remodeling may be a form of ribosome specialization and show that heterogeneous cytosolic polysomes accumulate after cold acclimation, leading to shifts in the translational output that differs between wild-type and reil-dkos. I found that heterogeneous complexes consist of newly synthesized and reused proteins. I propose that tailored ribosome complexes enable free 60S subunits to select specific 48S initiation complexes for translation. Cold acclimated ribosomes through ribosome remodeling synthesize a novel proteome consistent with known mechanisms of cold acclimation. The main hypothesis arising from my thesis is that heterogeneous/ specialized ribosomes alter translation preferences, adjust the proteome and thereby activate plant programs for successful cold acclimation.
The role of biogenic carbonate producers in the evolution of the geometries of carbonate systems has been the subject of numerous research projects. Attempts to classify modern and ancient carbonate systems by their biotic components have led to the discrimination of biogenic carbonate producers broadly into Photozoans, which are characterised by an affinity for warm tropical waters and high dependence on light penetration, and Heterozoans which are generally associated with both cool water environments and nutrient-rich settings with little to no light penetration. These broad categories of carbonate sediment producers have also been recognised to dominate in specific carbonate systems. Photozoans are commonly dominant in flat-topped platforms with steep margins, while Heterozoans generally dominate carbonate ramps. However, comparatively little is known on how these two main groups of carbonate producers interact in the same system and impact depositional geometries responding to changes in environmental conditions such as sea level fluctuation, antecedent slope, sediment transport processes, etc. This thesis presents numerical models to investigate the evolution of Miocene carbonate systems in the Mediterranean from two shallow marine domains: 1) a Miocene flat-topped platform dominated by Photozoans, with a significant component of Hetrozoans in the slope and 2) a Heterozoan distally steepened ramp, with seagrass-influenced (Photozoan) inner ramp. The overarching aim of the three articles comprising this cumulative thesis is to provide a numerical study of the role of Photozoans and Heterozoans in the evolution of carbonate system geometries and how these biotas respond to changes in environmental conditions. This aim was achieved using stratigraphic forward modelling, which provides an approach to quantitatively integrate multi-scale datasets to reconstruct sedimentary processes and products during the evolution of a sedimentary system.
In a Photozoan-dominated carbonate system, such as the Miocene Llucmajor platform in Western Mediterranean, stratigraphic forward modelling dovetailed with a robust set of sensitivity tests reveal how the geometry of the carbonate system is determined by the complex interaction of Heterozoan and Photozoan biotas in response to variable conditions of sea level fluctuation, substrate configuration, sediment transport processes and the dominance of Photozoan over Heterozoan production. This study provides an enhanced understanding of the different carbonate systems that are possible under different ecological and hydrodynamic conditions. The research also gives insight into the roles of different biotic associations in the evolution of carbonate geometries through time and space. The results further show that the main driver of platform progradation in a Llucmajor-type system is the lowstand production of Heterozoan sediments, which form the necessary substratum for Photozoan production.
In Heterozoan systems, sediment production is mainly characterised by high transport deposits, that are prone to redistribution by waves and gravity, thereby precluding the development of steep margins. However, in the Menorca ramp, the occurrence of sediment trapping by seagrass led to the evolution of distal slope steepening. We investigated, through numerical modelling, how such a seagrass-influenced ramp responds to the frequency and amplitude of sea level changes, variable carbonate production between the euphotic and oligophotic zone, and changes in the configuration of the paleoslope. The study reinforces some previous hypotheses and presents alternative scenarios to the established concepts of high-transport ramp evolution. The results of sensitivity experiments show that steep slopes are favoured in ramps that develop in high-frequency sea level fluctuation with amplitudes between 20 m and 40 m. We also show that ramp profiles are significantly impacted by the paleoslope inclination, such that an optimal antecedent slope of about 0.15 degrees is required for the Menorca distally steepened ramp to develop.
The third part presents an experimental case to argue for the existence of a Photozoan sediment threshold required for the development of steep margins in carbonate platforms. This was carried out by developing sensitivity tests on the forward models of the flat-topped (Llucmajor) platform and the distally steepened (Menorca) platform. The results show that models with Photozoan sediment proportion below a threshold of about 40% are incapable of forming steep slopes. The study also demonstrates that though it is possible to develop steep margins by seagrass sediment trapping, such slopes can only be stabilized by the appropriate sediment fabric and/or microbial binding. In the Photozoan-dominated system, the magnitude of slope steepness depends on the proportion of Photozoan sediments in the system. Therefore, this study presents a novel tool for characterizing carbonate systems based on their biogenic components.
Background: The role of fatty acid (FA) intake and metabolism in type 2 diabetes (T2D) incidence is controversial. Some FAs are not synthesised endogenously and, therefore, these circulating FAs reflect dietary intake, for example, the trans fatty acids (TFAs), saturated odd chain fatty acids (OCFAs), and linoleic acid, an n-6 polyunsaturated fatty acids (PUFA). It remains unclear if intake of TFA influence T2D risk and whether industrial TFAs (iTFAs) and ruminant TFAs (rTFAs) exert the same effect. Unlike even chain saturated FAs, the OCFAs have been inversely associated with T2D risk, but this association is poorly understood. Furthermore, the associations of n-6 PUFAs intake with T2D risk are still debated, while delta-5 desaturase (D5D), a key enzyme in the metabolism of PUFAs, has been consistently related to T2D risk. To better understand these relationships, the FA composition in circulating lipid fractions can be used as biomarkers of dietary intake and metabolism. The exploration of TFAs subtypes in plasma phospholipids and OCFAs and n-6 PUFAs within a wide range of lipid classes may give insights into the pathophysiology of T2D.
Aim: This thesis aimed mainly to analyse the association of TFAs, OCFAs and n-6 PUFAs with self-reported dietary intake and prospective T2D risk, using seven types of TFAs in plasma phospholipids and deep lipidomics profiling data from fifteen lipid classes.
Methods: A prospective case-cohort study was designed within the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam study, including all the participants who developed T2D (median follow-up 6.5 years) and a random subsample of the full cohort (subcohort: n=1248; T2D cases: n=820). The main analyses included two lipid profiles. The first was an assessment of seven TFA in plasma phospholipids, with a modified method for analysis of FA with very low abundances. The second lipid profile was derived from a high-throughout lipid profiling technology, which identified 940 distinct molecular species and allowed to quantify OCFAs and PUFAs composition across 15 lipid classes. Delta-5 desaturase (D5D) activity was estimated as 20:4/20:3-ratio. Using multivariable Cox regression models, we examined the associations of TFA subtypes with incident T2D and class-specific associations of OCFA and n-6 PUFAs with T2D risk.
Results: 16:1n-7t, 18:1n-7t, and c9t11-CLA were positively correlated with the intake of fat-rich dairy foods. iTFA 18:1 isomers were positively correlated with margarine. After adjustment for confounders and other TFAs, higher plasma phospholipid concentrations of two rTFAs were associated with a lower incidence of T2D: 18:1n-7t and t10c12-CLA. In contrast, the rTFA c9t11-CLA was associated with a higher incidence of T2D. rTFA 16:1n-7t and iTFAs (18:1n-6t, 18:1n-9t, 18:2n-6,9t) were not statistically significantly associated with T2D risk.
We observed heterogeneous integration of OCFA in different lipid classes, and the contribution of 15:0 versus 17:0 to the total OCFA abundance differed across lipid classes. Consumption of fat-rich dairy and fiber-rich foods were positively and red meat inversely correlated to OCFA abundance in plasma phospholipid classes. In women only, higher abundances of 15:0 in phosphatidylcholines (PC) and diacylglycerols (DG), and 17:0 in PC, lysophosphatidylcholines (LPC), and cholesterol esters (CE) were inversely associated with T2D risk. In men and women, a higher abundance of 15:0 in monoacylglycerols (MG) was also inversely associated with T2D. Conversely, a higher 15:0 concentration in LPC and triacylglycerols (TG) was associated with higher T2D risk in men. Women with a higher concentration of 17:0 as free fatty acids (FFA) also had higher T2D incidence.
The integration of n-6 PUFAs in lipid classes was also heterogeneous. 18:2 was highly abundant in phospholipids (particularly PC), CE, and TG; 20:3 represented a small fraction of FA in most lipid classes, and 20:4 accounted for a large proportion of circulating phosphatidylinositol (PI) and phosphatidylethanolamines (PE). Higher concentrations of 18:2 were inversely associated with T2D risk, especially within DG, TG, and LPC. However, 18:2 as part of MG was positively associated with T2D risk. Higher concentrations of 20:3 in phospholipids (PC, PE, PI), FFA, CE, and MG were linked to higher T2D incidence. 20:4 was unrelated to risk in most lipid classes, except positive associations were observed for 20:4 enriched in FFA and PE. The estimated D5D activities in PC, PE, PI, LPC, and CE were inversely associated with T2D and explained variance of estimated D5D activity by genomic variation in the FADS locus was only substantial in those lipid classes.
Conclusion: The TFAs' conformation is essential in their relationship to diabetes risk, as indicated by plasma rTFA subtypes concentrations having opposite directions of associations with diabetes risk. Plasma OCFA concentration is linked to T2D risk in a lipid class and sex-specific manner. Plasma n-6 PUFA concentrations are associated differently with T2D incidence depending on the specific FA and the lipid class. Overall, these results highlight the complexity of circulating FAs and their heterogeneous association with T2D risk depending on the specific FA structure, lipid class, and sex. My results extend the evidence of the relationship between diet, lipid metabolism, and subsequent T2D risk. In addition, my work generated several potential new biomarkers of dietary intake and prospective T2D risk.
The central gas in half of all galaxy clusters shows short cooling times. Assuming unimpeded cooling, this should lead to high star formation and mass cooling rates, which are not observed. Instead, it is believed that condensing gas is accreted by the central black hole that powers an active galactic nuclei jet, which heats the cluster. The detailed heating mechanism remains uncertain. A promising mechanism invokes cosmic ray protons that scatter on self-generated magnetic fluctuations, i.e. Alfvén waves. Continuous damping of Alfvén waves provides heat to the intracluster medium. Previous work has found steady state solutions for a large sample of clusters where cooling is balanced by Alfvénic wave heating. To verify modeling assumptions, we set out to study cosmic ray injection in three-dimensional magnetohydrodynamical simulations of jet feedback in an idealized cluster with the moving-mesh code arepo. We analyze the interaction of jet-inflated bubbles with the turbulent magnetized intracluster medium.
Furthermore, jet dynamics and heating are closely linked to the largely unconstrained jet composition. Interactions of electrons with photons of the cosmic microwave background result in observational signatures that depend on the bubble content. Those recent observations provided evidence for underdense bubbles with a relativistic filling while adopting simplifying modeling assumptions for the bubbles. By reproducing the observations with our simulations, we confirm the validity of their modeling assumptions and as such, confirm the important finding of low-(momentum) density jets.
In addition, the velocity and magnetic field structure of the intracluster medium have profound consequences for bubble evolution and heating processes. As velocity and magnetic fields are physically coupled, we demonstrate that numerical simulations can help link and thereby constrain their respective observables. Finally, we implement the currently preferred accretion model, cold accretion, into the moving-mesh code arepo and study feedback by light jets in a radiatively cooling magnetized cluster. While self-regulation is attained independently of accretion model, jet density and feedback efficiencies, we find that in order to reproduce observed cold gas morphology light jets are preferred.
Background: The characteristics of osteoporosis are decreased bone mass and destruction towards the microarchitecture of bone tissue, which raises the risk of fracture. Psychosocialstress and osteoporosis are linked by sympathetic nervous system, hypothalamic-pituitary-adrenal axis, and other endocrine factors. Psychosocial stress causes a series of effects on the organism, and this long-term depletion at the cellular level is considered to be mitochondrial allostatic load, including mitochondrial dysfunction and oxidative stress. Extracellular vesicles (EVs) are involved in the mitochondrial allostatic load process and may as biomarkers in this setting. As critical participants during cell-to-cell communications, EVs serve as transport vehicles for nucleic acid and proteins, alter the phenotypic and functional characteristics of their target cells, and promote cell-to-cell contact. And hence, they play a significant role in the diagnosis and therapy of many diseases, such as osteoporosis.
Aim: This narrative review attempts to outline the features of EVs, investigate their involvement in both psychosocial stress and osteoporosis, and analyze if EVs can be potential mediators between both.
Methods: The online database from PubMed, Google Scholar, and Science Direct were searched for keywords related to the main topic of this study, and the availability of all the selected studies was verified. Afterward, the findings from the articles were summarized and synthesized.
Results: Psychosocial stress affects bone remodeling through increased neurotransmitters such as glucocorticoids and catecholamines, as well as increased glucose metabolism. Furthermore, psychosocial stress leads to mitochondrial allostatic load, including oxidative stress, which may affect bone remodeling. In vitro and in vivo data suggest EVs might involve in the link between psychosocial stress and bone remodeling through the transfer of bioactive substances and thus be a potential mediator of psychosocial stress leading to osteoporosis.
Conclusions: According to the included studies, psychosocial stress affects bone remodeling, leading to osteoporosis. By summarizing the specific properties of EVs and the function of EVs in both psychosocial stress and osteoporosis, respectively, it has been demonstrated that EVs are possible mediators of both, and have the prospects to be useful in innovative research areas.
Biogeochemical analyses of lacustrine environments are well-established methods that allow exploring and understanding complex systems in the lake ecosystem. However, most were conducted in temperate lakes controlled by entirely different physical conditions than in tropical climates. The most important difference between the temperate and tropical lakes is lacking seasonal temperature fluctuations in the latter, which leads to a stable temperature gradient in the water column. Thus, the water column in tropical latitudes generally is void of perturbations that can be seen in their temperate counterparts. Permanent stratification in the water column provides optimal conditions for intact sedimentation. The geochemical processes in the water column and the weathering process in the distinct lithology in the catchment leads to the different biogeochemical characteristic in the sediment. Conducting a biogeochemical study in this lake sediment, especially in the Sediment Water Interface (SWI) helps reveal the sedimentation and diagenetic process records influenced by the internal or external loading. Lake Sentani, the study area, is one of the thousands of lakes in Indonesia and located in the Papua province. This tropical lake has a unique feature, as it consists of four interconnected sub-basins with different water depths. More importantly, its catchment is comprised of various different lithologies. Hence, its lithological characteristics are highly diverse, and range from mafic and ultramafic rocks to clastic sediment and carbonates. Each sub-basin receives a distinct sediment input. Equally important, besides the natural loading, Lake Sentani is also influenced by anthropogenic input. Previous studies have elaborated that there is an increase in population growth rate around the lake which has direct consequences on eutrophication. Considering these factors, the government of The Republic of Indonesia put Lake Sentani on the list of national priority lakes for restoration. This thesis aims to develop a fundamental understanding of Lake Sentani's sedimentary geochemistry and geomicrobiology with a special focus on the effects of different lithologies and anthropogenic pressures in the catchment area. We conducted geochemical and geomicrobiology research on Lake Sentani to meet this objective. We investigated geochemical characteristics in the water column, porewater, and sediment core of the four sub-basins. Additional to direct investigations of the lake itself, we also studied the sediments in the tributary rivers, of which some are ephemeral, as well as the river mouths, as connections between riverine and the lacustrine habitat. The thesis is composed of three main publications about Lake Sentani and supported by several publications that focus on other tropical lakes in Indonesia. The first main publication investigates the geochemical characterization of the water column, porewater, and surface sediment (upper 40-50 cm) from the center of the four sub-basins. It reveals that besides catchment lithology, the water column heavily influences the geochemical characteristics in the lake sediments and their porewater. The findings indicate that water column stratification has a strong influence on overall chemistry. The four sub-basins are very different with regard to their water column chemistry. Based on the physicochemical profiles, especially dissolved oxygen, one sub-basin is oxygenated, one intermediate i.e. just reaches oxygen depletion at the sediment-water interface, and two sub-basins are fully meromictic. However, all four sub-basins share the same surface water chemistry. The structure of the water column creates differences on the patterns of anions and cations in the porewater. Likewise, the distinct differences in geochemical composition between the sub-basins show that the lithology in the catchment affects the geochemical characteristic in the sediment. Overall, water column stratification and particularly bottom water oxygenation strongly influence the overall elemental composition of the sediment and porewater composition. The second publication reveals differences in surface sediment composition between habitats, influenced by lithological variations in the catchment area. The macro-element distribution shows that the geochemical characteristics between habitats are different. Furthermore, the geochemical composition also indicates a distinct distribution between the sub-basins. The geochemical composition of the eastern sub-basin suggests that lithogenic elements are more dominant than authigenic elements. This is also supported by sulfide speciation, particle distribution, and smear slide data. The third publication is a geomicrobiological study of the surface sediment. We compare the geochemical composition of the surface sediment and its microbiological composition and compare the different signals. Next Generation Sequencing (NGS) of the 16S rRNA gene was applied to determine the microbial community composition of the surface sediment from a great number of locations. We use a large number of sampling sites in all four sub-basins as well as in the rivers and river mouths to illustrate the links between the river, the river mouth, and the lake. Rigorous assessment of microbial communities across the diverse Lake Sentani habitats allowed us to study some of these links and report novel findings on microbial patterns in such ecosystems. The main result of the Principal Coordinates Analysis (PCoA) based on microbial community composition highlighted some commonalities but also differences between the microbial community analysis and the geochemical data. The microbial community in rivers, river mouths and sub-basins is strongly influenced by anthropogenic input from the catchment area. Generally, Bacteroidetes and Firmicutes could be an indicator for river sediments. The microbial community in the river is directly influenced by anthropogenic pressure and is markedly different from the lake sediment. Meanwhile, the microbial community in the lake sediment reflects the anoxic environment, which is prevalent across the lake in all sediments below a few mm burial depth. The lake sediments harbour abundant sulfate reducers and methanogens. The microbial communities in sediments from river mouths are influenced by both rivers and lake ecosystems. This study provides valuable information to understand the basic processes that control biogeochemical cycling in Lake Sentani. Our findings are critical for lake managers to accurately assess the uncertainties of the changing environmental conditions related to the anthropogenic pressure in the catchment area. Lake Sentani is a unique study site directly influenced by the different geology across the watershed and morphometry of the four studied basins. As a result of these factors, there are distinct geochemical differences between the habitats (river, river mouth, lake) and the four sub-basins. In addition to geochemistry, microbial community composition also shows differences between habitats, although there are no obvious differences between the four sub-basins. However, unlike sediment geochemistry, microbial community composition is impacted by human activities. Therefore, this thesis will provide crucial baseline data for future lake management.
Im Rahmen dieser Dissertation wurden die erstmaligen Totalsynthesen der Arylnaphthalen-Lignane Alashinol D, Vitexdoin C, Vitrofolal E, Noralashinol C1 und Ternifoliuslignan E vorgestellt. Der Schlüsselschritt der entwickelten Methode, basiert auf einer regioselektiven intramolekularen Photo-Dehydro-Diels-Alder (PDDA)-Reaktion, die mittels UV-Strahlung im Durchflussreaktor durchgeführt wurde. Bei der Synthese der PDDA-Vorläufer (Diarylsuberate) wurde eine Synthesestrategie nach dem Baukastenprinzip verfolgt. Diese ermöglicht die Darstellung asymmetrischer komplexer Systeme aus nur wenigen Grundbausteinen und die Totalsynthese einer Vielzahl an Lignanen. In systematischen Voruntersuchungen konnte zudem die klare Überlegenheit der intra- gegenüber der intermolekularen PDDA-Reaktion aufgezeigt werden. Dabei stellte sich eine Verknüpfung der beiden Arylpropiolester über einen Korksäurebügel, in para-Position, als besonders effizient heraus. Werden asymmetrisch substituierte Diarylsuberate, bei denen einer der endständigen Estersubstituenten durch eine Trimethylsilyl-Gruppe oder ein Wasserstoffatom ersetzt wurde, verwendet, durchlaufen diese Systeme eine regioselektive Cyclisierung und als Hauptprodukt werden Naphthalenophane mit einem Methylester in 3-Position erhalten. Mit Hilfe von umfangreichen Experimenten zur Funktionalisierung der 4-Position, konnte zudem gezeigt werden, dass die Substitution der nucleophilen Cycloallen-Intermediate, während der PDDA-Reaktion, generell durch die Zugabe von N-Halogen-Succinimiden möglich ist. In Anbetracht der geringen Ausbeuten haben diese intermolekularen Abfangreaktionen, jedoch keinen präparativen Nutzen für die Totalsynthesen von Lignanen. Mit dem Ziel die allgemeinen photochemischen Reaktionsbedingungen zu optimieren, wurde erstmalig die triplettsensibilisierte PDDA-Reaktion vorgestellt. Durch die Verwendung von Xanthon als Sensibilisator wurde der Einsatz von effizienteren UVA-Lichtquellen ermöglicht, wodurch die Gefahr einer Photozersetzung durch Überbestrahlung minimiert wurde. Im Vergleich zur direkten Anregung mit UVB-Strahlung, konnten die Ausbeuten mit indirekter Anregung durch einen Photokatalysator signifikant gesteigert werden. Die grundlegenden Erkenntnisse und die entwickelten Synthesestrategien dieser Arbeit, können dazu beitragen zukünftig die Erschließung neuer pharmakologisch interessanter Lignane voranzutreiben.
1 Bisher ist nur die semisynthetische Darstellung von Noralashinol C ausgehend von Hydroxymatairesinol literaturbekannt.
In recent decades, astronomy has seen a boom in large-scale stellar surveys of the Galaxy. The detailed information obtained about millions of individual stars in the Milky Way is bringing us a step closer to answering one of the most outstanding questions in astrophysics: how do galaxies form and evolve? The Milky Way is the only galaxy where we can dissect many stars into their high-dimensional chemical composition and complete phase space, which analogously as fossil records can unveil the past history of the genesis of the Galaxy. The processes that lead to large structure formation, such as the Milky Way, are critical for constraining cosmological models; we call this line of study Galactic archaeology or near-field cosmology.
At the core of this work, we present a collection of efforts to chemically and dynamically characterise the disks and bulge of our Galaxy. The results we present in this thesis have only been possible thanks to the advent of the Gaia astrometric satellite, which has revolutionised the field of Galactic archaeology by precisely measuring the positions, parallax distances and motions of more than a billion stars. Another, though not less important, breakthrough is the APOGEE survey, which has observed spectra in the near-infrared peering into the dusty regions of the Galaxy, allowing us to determine detailed chemical abundance patterns in hundreds of thousands of stars. To accurately depict the Milky Way structure, we use and develop the Bayesian isochrone fitting tool/code called StarHorse; this software can predict stellar distances, extinctions and ages by combining astrometry, photometry and spectroscopy based on stellar evolutionary models. The StarHorse code is pivotal to calculating distances where Gaia parallaxes alone cannot allow accurate estimates.
We show that by combining Gaia, APOGEE, photometric surveys and using StarHorse, we can produce a chemical cartography of the Milky way disks from their outermost to innermost parts. Such a map is unprecedented in the inner Galaxy. It reveals a continuity of the bimodal chemical pattern previously detected in the solar neighbourhood, indicating two populations with distinct formation histories. Furthermore, the data reveals a chemical gradient within the thin disk where the content of 𝛼-process elements and metals is higher towards the centre. Focusing on a sample in the inner MW we confirm the extension of the chemical duality to the innermost regions of the Galaxy. We find stars with bar shape orbits to show both high- and low-𝛼 abundances, suggesting the bar formed by secular evolution trapping stars that already existed. By analysing the chemical orbital space of the inner Galactic regions, we disentangle the multiple populations that inhabit this complex region. We reveal the presence of the thin disk, thick disk, bar, and a counter-rotating population, which resembles the outcome of a perturbed proto-Galactic disk. Our study also finds that the inner Galaxy holds a high quantity of super metal-rich stars up to three times solar suggesting it is a possible repository of old super-metal-rich stars found in the solar neighbourhood.
We also enter into the complicated task of deriving individual stellar ages. With StarHorse, we calculate the ages of main-sequence turn-off and sub-giant stars for several public spectroscopic surveys. We validate our results by investigating linear relations between chemical abundances and time since the 𝛼 and neutron capture elements are sensitive to age as a reflection of the different enrichment timescales of these elements. For further study of the disks in the solar neighbourhood, we use an unsupervised machine learning algorithm to delineate a multidimensional separation of chrono-chemical stellar groups revealing the chemical thick disk, the thin disk, and young 𝛼-rich stars. The thick disk is shown to have a small age dispersion indicating its fast formation contrary to the thin disk that spans a wide range of ages.
With groundbreaking data, this thesis encloses a detailed chemo-dynamical view of the disk and bulge of our Galaxy. Our findings on the Milky Way can be linked to the evolution of high redshift disk galaxies, helping to solve the conundrum of galaxy formation.
Following the extinction of dinosaurs, the great adaptive radiation of mammals occurred, giving rise to an astonishing ecological and phenotypic diversity of mammalian species. Even closely related species often inhabit vastly different habitats, where they encounter diverse environmental challenges and are exposed to different evolutionary pressures. As a response, mammals evolved various adaptive phenotypes over time, such as morphological, physiological and behavioural ones. Mammalian genomes vary in their content and structure and this variation represents the molecular mechanism for the long-term evolution of phenotypic variation. However, understanding this molecular basis of adaptive phenotypic variation is usually not straightforward.
The recent development of sequencing technologies and bioinformatics tools has enabled a better insight into mammalian genomes. Through these advances, it was acknowledged that mammalian genomes differ more, both within and between species, as a consequence of structural variation compared to single-nucleotide differences. Structural variant types investigated in this thesis - such as deletion, duplication, inversion and insertion, represent a change in the structure of the genome, impacting the size, copy number, orientation and content of DNA sequences. Unlike short variants, structural variants can span multiple genes. They can alter gene dosage, and cause notable gene expression differences and subsequently phenotypic differences. Thus, they can lead to a more dramatic effect on the fitness (reproductive success) of individuals, local adaptation of populations and speciation.
In this thesis, I investigated and evaluated the potential functional effect of structural variations on the genomes of mustelid species. To detect the genomic regions associated with phenotypic variation I assembled the first reference genome of the tayra (Eira barbara) relying on linked-read sequencing technology to achieve a high level of genome completeness important for reliable structural variant discovery. I then set up a bioinformatics pipeline to conduct a comparative genomic analysis and explore variation between mustelid species living in different environments. I found numerous genes associated with species-specific phenotypes related to diet, body condition and reproduction among others, to be impacted by structural variants.
Furthermore, I investigated the effects of artificial selection on structural variants in mice selected for high fertility, increased body mass and high endurance. Through selective breeding of each mouse line, the desired phenotypes have spread within these populations, while maintaining structural variants specific to each line. In comparison to the control line, the litter size has doubled in the fertility lines, individuals in the high body mass lines have become considerably larger, and mice selected for treadmill performance covered substantially more distance. Structural variants were found in higher numbers in these trait-selected lines than in the control line when compared to the mouse reference genome. Moreover, we have found twice as many structural variants spanning protein-coding genes (specific to each line) in trait-selected lines. Several of these variants affect genes associated with selected phenotypic traits. These results imply that structural variation does indeed contribute to the evolution of the selected phenotypes and is heritable.
Finally, I suggest a set of critical metrics of genomic data that should be considered for a stringent structural variation analysis as comparative genomic studies strongly rely on the contiguity and completeness of genome assemblies. Because most of the available data used to represent reference genomes of mammalian species is generated using short-read sequencing technologies, we may have incomplete knowledge of genomic features. Therefore, a cautious structural variation analysis is required to minimize the effect of technical constraints.
The impact of structural variants on the adaptive evolution of mammalian genomes is slowly gaining more focus but it is still incorporated in only a small number of population studies. In my thesis, I advocate the inclusion of structural variants in studies of genomic diversity for a more comprehensive insight into genomic variation within and between species, and its effect on adaptive evolution.
Cosmic rays (CRs) constitute an important component of the interstellar medium (ISM) of galaxies and are thought to play an essential role in governing their evolution. In particular, they are able to impact the dynamics of a galaxy by driving galactic outflows or heating the ISM and thereby affecting the efficiency of star-formation. Hence, in order to understand galaxy formation and evolution, we need to accurately model this non-thermal constituent of the ISM. But except in our local environment within the Milky Way, we do not have the ability to measure CRs directly in other galaxies. However, there are many ways to indirectly observe CRs via the radiation they emit due to their interaction with magnetic and interstellar radiation fields as well as with the ISM.
In this work, I develop a numerical framework to calculate the spectral distribution of CRs in simulations of isolated galaxies where a steady-state between injection and cooling is assumed. Furthermore, I calculate the non-thermal emission processes arising from the modelled CR proton and electron spectra ranging from radio wavelengths up to the very high-energy gamma-ray regime.
I apply this code to a number of high-resolution magneto-hydrodynamical (MHD) simulations of isolated galaxies, where CRs are included. This allows me to study their CR spectra and compare them to observations of the CR proton and electron spectra by the Voyager-1 satellite and the AMS-02 instrument in order to reveal the origin of the measured spectral features.
Furthermore, I provide detailed emission maps, luminosities and spectra of the non-thermal emission from our simulated galaxies that range from dwarfs to Milk-Way analogues to starburst galaxies at different evolutionary stages. I successfully reproduce the observed relations between the radio and gamma-ray luminosities with the far-infrared (FIR) emission of star-forming (SF) galaxies, respectively, where the latter is a good tracer of the star-formation rate. I find that highly SF galaxies are close to the limit where their CR population would lose all of their energy due to the emission of radiation, whereas CRs tend to escape low SF galaxies more quickly. On top of that, I investigate the properties of CR transport that are needed in order to match the observed gamma-ray spectra.
Furthermore, I uncover the underlying processes that enable the FIR-radio correlation (FRC) to be maintained even in starburst galaxies and find that thermal free-free-emission naturally explains the observed radio spectra in SF galaxies like M82 and NGC 253 thus solving the riddle of flat radio spectra that have been proposed to contradict the observed tight FRC.
Lastly, I scrutinise the steady-state modelling of the CR proton component by investigating for the first time the influence of spectrally resolved CR transport in MHD simulations on the hadronic gamma-ray emission of SF galaxies revealing new insights into the observational signatures of CR transport both spectrally and spatially.