570 Biowissenschaften; Biologie
Refine
Year of publication
Document Type
- Article (1026)
- Doctoral Thesis (656)
- Postprint (413)
- Other (52)
- Review (40)
- Habilitation Thesis (19)
- Conference Proceeding (9)
- Master's Thesis (8)
- Monograph/Edited Volume (7)
- Part of Periodical (7)
Keywords
- Arabidopsis thaliana (35)
- climate change (27)
- Arabidopsis (23)
- ancient DNA (21)
- Dictyostelium (20)
- evolution (20)
- biodiversity (18)
- coexistence (16)
- diversity (15)
- metabolomics (14)
Institute
- Institut für Biochemie und Biologie (1713)
- Institut für Ernährungswissenschaft (232)
- Mathematisch-Naturwissenschaftliche Fakultät (120)
- Extern (82)
- Institut für Chemie (52)
- Institut für Geowissenschaften (29)
- Institut für Physik und Astronomie (26)
- Institut für Umweltwissenschaften und Geographie (23)
- Department Sport- und Gesundheitswissenschaften (12)
- Fakultät für Gesundheitswissenschaften (9)
Lafora disease (LD, OMIM #254780) is a rare, recessively inherited neurodegenerative disease with adolescent onset, resulting in progressive myoclonus epilepsy which is fatal usually within ten years of symptom onset. The disease is caused by loss-of-function mutations in either of the two genes EPM2A (laforin) or EPM2B (malin). It characteristically involves the accumulation of insoluble glycogen-derived particles, named Lafora bodies (LBs), which are considered neurotoxic and causative of the disease. The pathogenesis of LD is therefore centred on the question of how insoluble LBs emerge from soluble glycogen. Recent data clearly show that an abnormal glycogen chain length distribution, but neither hyperphosphorylation nor impairment of general autophagy, strictly correlates with glycogen accumulation and the presence of LBs. This review summarizes results obtained with patients, mouse models, and cell lines and consolidates apparent paradoxes in the LD literature. Based on the growing body of evidence, it proposes that LD is predominantly caused by an impairment in chain-length regulation affecting only a small proportion of the cellular glycogen. A better grasp of LD pathogenesis will further develop our understanding of glycogen metabolism and structure. It will also facilitate the development of clinical interventions that appropriately target the underlying cause of LD.
Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis.
While habitat loss is a known key driver of biodiversity decline, the impact of other landscape properties, such as patch isolation, is far less clear. When patch isolation is low, species may benefit from a broader range of foraging opportunities, but are at the same time adversely affected by higher predation pressure from mobile predators. Although previous approaches have successfully linked such effects to biodiversity, their impact on local and metapopulation dynamics has largely been ignored. Since population dynamics may also be affected by environmental disturbances that temporally change the degree of patch isolation, such as periodic changes in habitat availability, accurate assessment of its link with isolation is highly challenging. To analyze the effect of patch isolation on the population dynamics on different spatial scales, we simulate a three-species meta-food chain on complex networks of habitat patches and assess the average variability of local populations and metapopulations, as well as the level of synchronization among patches. To evaluate the impact of periodic environmental disturbances, we contrast simulations of static landscapes with simulations of dynamic landscapes in which 30 percent of the patches periodically become unavailable as habitat. We find that increasing mean patch isolation often leads to more asynchronous population dynamics, depending on the parameterization of the food chain. However, local population variability also increases due to indirect effects of increased dispersal mortality at high mean patch isolation, consequently destabilizing metapopulation dynamics and increasing extinction risk. In dynamic landscapes, periodic changes of patch availability on a timescale much slower than ecological interactions often fully synchronize the dynamics. Further, these changes not only increase the variability of local populations and metapopulations, but also mostly overrule the effects of mean patch isolation. This may explain the often small and inconclusive impact of mean patch isolation in natural ecosystems.
(1) Environmental conditions experienced in the past may lead to intraspecific differences in ecological and chemical traits of plants, which likely affect future responses to altered or new environments. Whether competition by neighbors is such a trait-shaping factor is not yet well-known. We aimed to understand how the level of ancestral plant competition affects traits related to plant fitness and resource allocation, reproduction, and (phyto-)toxin accumulation in offspring, and whether a potential differentiation in these traits can be found in different geographic origins of which one belongs to the native and one to the invaded range. (2) We compared differentiation of the following traits in offspring plants of multiple populations in Erodium cicutarium (Geraniaceae): biomass, seed production, seed traits related to dispersal and germination, and concentrations of foliar mono- and sesquiterpenes. We tested the allelopatic potential of aqueous extracts of the same E. cicutarium plants on seeds of five different plant families. (3) In plants originating from populations that experienced high levels of competition, we found twice as high monoterpene concentrations. These plants also produced more biomass and a higher proportion of ripe to unripe seeds until harvesting. Seeds originating from high competition sites were shorter. Aqueous E. cicutarium leaf extracts with high terpenoid content reduced radicle length of Zea mays and radicle and hypocotyl length of E. cicutarium seedlings. (4) The results of this study provide first evidence that the surrounding vegetation may shape chemo-ecological plant traits that may be fundamental for competitive ability. Our study calls for more research testing whether competition experienced in the native range may lead to an enhanced capability of plants to establish populations and spread in a new range.
Past and present biodiversity in northeastern Siberia inferred from sedimentary DNA metabarcoding
(2021)
The arctic-boreal treeline is a transition zone from taiga to tundra covering a vast area in Siberia. It often features large environmental gradients and reacts sensitively to changes in the environment. For example, the expansion of shrubs and a northward movement of the treeline are observable in Siberia as a response to the warming climate. The changes in vegetation across the treeline are known to influence the water chemistry in the lakes. This causes further alteration to the composition and diversity of sensitive aquatic organisms such as diatoms and macrophytes. Despite the rising awareness of the complex climate-feedback mechanisms of terrestrial plants, the understanding of their assembly rules and about responses of aquatic biomes in the surrounding treeline lakes is still limited. The goal of this thesis is to examine the previous and present biodiversity of terrestrial and freshwater biomes from the Siberian treeline ecotone, as well as their reactions to environmental changes. In particular, this thesis attempts to examine the performance of applying sedimentary DNA metabarcoding in terrestrial plants, aquatic macrophytes and diatoms, their spatial patterns along the environmental gradients and their temporal patterns throughout the climate transition from the late Pleistocene to Holocene. Sedimentary DNA metabarcoding combined with next-generation sequencing is applied as a primary tool to explore the composition and diversity of terrestrial plants, diatoms and aquatic macrophytes. The main study area is located in Chukotka of northeastern Siberia in the Arctic, a biodiversity hotspot due to its continental location and the diverse habitats of the glacial refugium. The modern diatom diversity was assessed with a specific diatom metabarcoding marker and morphological identification. Both approaches agree to a dominance of Fragilariaceae and Aulacoseiraceae, as well as on the environmental influential indicators of the diatom community. The high diversity of Fragilariaceae identified in the thermokarst lakes is found to follow the vegetation gradient along the treeline, suggesting that diatom metabarcoding can decipher relationships between diatom assemblage shifts and the relevant environmental changes. In particular, the metabarcoding approach detects diversification of fragilarioids in glacial lakes which is not visible using morphology. Sedimentary ancient DNA records indicate a vegetation mosaic of forb-dominated steppe-tundra during 28-19 ka, followed by a shift to dwarf-shrub tundra during 19-14 ka. During the most recent 14 thousand years, the vegetation consists of deciduous shrublands, then a change to boreal forest is observed. Investigations on the alpha diversity of the vegetation show that species richness is unexpectedly highest during pre-LGM, which is likely related to the extensive area that allows for more taxa. The optimum Holocene warming during 9-6 ka is not accompanied by a high richness as widely believed, but with an evenly distributed community by the fulfilment of erect shrubs. Furthermore, changes in taxonomic and phylogenetic diversity show complementary results in understanding community diversity. The composition and richness in the modern macrophytes community from Siberian Arctic and Chinese alpine are best co-influenced by July temperature and electrical conductivity.. Past macrophyte turnover during the late Pleistocene-Holocene is less noticeable in Siberia, whereas a pronounced community change from emergent to submerged plants is detected from Chinese alpine regions at about 14 ka due to increasing temperature and varying water conductivity. Finally, sedimentary DNA metabarcoding is a cost-effective and powerful proxy for ecological application, whereas completeness of the reference library, coverage and resolution of the metabarcoding marker are the major limitations of sedimentary DNA based diversity monitoring. The composition and richness in modern vegetation and macrophytes across broad spatial gradients is constrained by environmental variables, suggesting a potential usage for environmental monitoring. Diatom distributions are driven by different water variables along the treeline. Past records indicate that the shrub coverage has a noticeable influence on the assemblies of both terrestrial plants and aquatic macrophytes, though the shift in macrophyte community is relatively minor in the past 28 thousand years. In the long-term, the shrub expansion may eventually result in a genetically more diverse vegetation community but reduced species richness. When exceeding the optimal temperatures, further warming may lead to a decrease and putative loss of macrophytes and diatoms.
Introduction: Many semiarid regions around the world are presently experiencing significant changes in both climatic conditions and vegetation. This includes a disturbed coexistence between grasses and bushes also known as bush encroachment, and altered precipitation patterns with larger rain events. Fewer, more intense precipitation events might promote groundwater recharge, but depending on the structure of the vegetation also encourage further woody encroachment.
Materials and Methods: In this study, we investigated how patterns and sources of water uptake of Acacia mellifera (blackthorn), an important encroaching woody plant in southern African savannas, are associated with the intensity of rain events and the size of individual shrubs. The study was conducted at a commercial cattle farm in the semiarid Kalahari in Namibia (MAP 250 mm/a). We used soil moisture dynamics in different depths and natural stable isotopes as markers of water sources. Xylem water of fifteen differently sized individuals during eight rain events was extracted using a Scholander pressure bomb.
Results and Discussion: Results suggest the main rooting activity zone of A. mellifera in 50 and 75 cm soil depth but a reasonable water uptake from 10 and 25 cm. Any apparent uptake pattern seems to be driven by water availability, not time in the season. Bushes prefer the deeper soil layers after heavier rain events, indicating some evidence for the classical Walter’s two-layer hypothesis. However, rain events up to a threshold of 6 mm/day cause shallower depths of use and suggest several phases of intense competition with perennial grasses. The temporal uptake pattern does not depend on shrub size, suggesting a fast upwards water flow inside. d2H and d18O values in xylem water indicate that larger shrubs rely less on upper and very deep soil water than smaller shrubs. It supports the hypothesis that in environments where soil moisture is highly variable in the upper soil layers, the early investment in a deep tap-root to exploit deeper, more reliable water sources could reduce the probability of mortality during the establishment phase. Nevertheless, independent of size and time in the season, bushes do not compete with potential groundwater recharge. In a savanna encroached by A. mellifera, groundwater will most likely be affected indirectly.
Introduction: Many semiarid regions around the world are presently experiencing significant changes in both climatic conditions and vegetation. This includes a disturbed coexistence between grasses and bushes also known as bush encroachment, and altered precipitation patterns with larger rain events. Fewer, more intense precipitation events might promote groundwater recharge, but depending on the structure of the vegetation also encourage further woody encroachment.
Materials and Methods: In this study, we investigated how patterns and sources of water uptake of Acacia mellifera (blackthorn), an important encroaching woody plant in southern African savannas, are associated with the intensity of rain events and the size of individual shrubs. The study was conducted at a commercial cattle farm in the semiarid Kalahari in Namibia (MAP 250 mm/a). We used soil moisture dynamics in different depths and natural stable isotopes as markers of water sources. Xylem water of fifteen differently sized individuals during eight rain events was extracted using a Scholander pressure bomb.
Results and Discussion: Results suggest the main rooting activity zone of A. mellifera in 50 and 75 cm soil depth but a reasonable water uptake from 10 and 25 cm. Any apparent uptake pattern seems to be driven by water availability, not time in the season. Bushes prefer the deeper soil layers after heavier rain events, indicating some evidence for the classical Walter’s two-layer hypothesis. However, rain events up to a threshold of 6 mm/day cause shallower depths of use and suggest several phases of intense competition with perennial grasses. The temporal uptake pattern does not depend on shrub size, suggesting a fast upwards water flow inside. d2H and d18O values in xylem water indicate that larger shrubs rely less on upper and very deep soil water than smaller shrubs. It supports the hypothesis that in environments where soil moisture is highly variable in the upper soil layers, the early investment in a deep tap-root to exploit deeper, more reliable water sources could reduce the probability of mortality during the establishment phase. Nevertheless, independent of size and time in the season, bushes do not compete with potential groundwater recharge. In a savanna encroached by A. mellifera, groundwater will most likely be affected indirectly.
Many studies on bacterial community composition (BCC) do not distinguish between particle associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. "Shannon and Simpson indices" showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently.
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
Dictyostelium cells undergo a semi-closed mitosis, during which the nuclear envelope (NE) persists; however, free diffusion between the cytoplasm and the nucleus takes place. To permit the formation of the mitotic spindle, the nuclear envelope must be permeabilized in order to allow diffusion of tubulin dimers and spindle assembly factors into the nucleus. In Aspergillus, free diffusion of proteins between the cytoplasm and the nucleus is achieved by a partial disassembly of the nuclear pore complexes (NPCs) prior to spindle assembly. In order to determine whether this is also the case in Dictyostelium, we analysed components of the NPC by immunofluorescence microscopy and live cell imaging and studied their behaviour during interphase and mitosis. We observed that the NPCs are absent from the contact area of the nucleoli and that some nucleoporins also localize to the centrosome and the spindle poles. In addition, we could show that, during mitosis, the central FG protein NUP62, two inner ring components and Gle1 depart from the NPCs, while all other tested NUPs remained at the NE. This leads to the conclusion that indeed a partial disassembly of the NPCs takes place, which contributes to permeabilisation of the NE during semi-closed mitosis.
Dictyostelium cells undergo a semi-closed mitosis, during which the nuclear envelope (NE) persists; however, free diffusion between the cytoplasm and the nucleus takes place. To permit the formation of the mitotic spindle, the nuclear envelope must be permeabilized in order to allow diffusion of tubulin dimers and spindle assembly factors into the nucleus. In Aspergillus, free diffusion of proteins between the cytoplasm and the nucleus is achieved by a partial disassembly of the nuclear pore complexes (NPCs) prior to spindle assembly. In order to determine whether this is also the case in Dictyostelium, we analysed components of the NPC by immunofluorescence microscopy and live cell imaging and studied their behaviour during interphase and mitosis. We observed that the NPCs are absent from the contact area of the nucleoli and that some nucleoporins also localize to the centrosome and the spindle poles. In addition, we could show that, during mitosis, the central FG protein NUP62, two inner ring components and Gle1 depart from the NPCs, while all other tested NUPs remained at the NE. This leads to the conclusion that indeed a partial disassembly of the NPCs takes place, which contributes to permeabilisation of the NE during semi-closed mitosis.
Mathematical analysis of partial differential equations (PDEs) has led to many insights regarding the effect of organism movements on spatial population dynamics. However, their use has mainly been confined to the community of mathematical biologists, with less attention from statistical and empirical ecologists. We conjecture that this is principally due to the inherent difficulties in fitting PDEs to data. To help remedy this situation, in the context of movement ecology, we show how the popular technique of step selection analysis (SSA) can be used to parametrize a class of PDEs, calleddiffusion-taxismodels, from an animal's trajectory. We examine the accuracy of our technique on simulated data, then demonstrate the utility of diffusion-taxis models in two ways. First, for non-interacting animals, we derive the steady-state utilization distribution in a closed analytic form. Second, we give a recipe for deriving spatial pattern formation properties that emerge from interacting animals: specifically, do those interactions cause heterogeneous spatial distributions to emerge and if so, do these distributions oscillate at short times or emerge without oscillations? The second question is applied to data on concurrently tracked bank volesMyodes glareolus. Our results show that SSA can accurately parametrize diffusion-taxis equations from location data, providing the frequency of the data is not too low. We show that the steady-state distribution of our diffusion-taxis model, where it is derived, has an identical functional form to the utilization distribution given by resource selection analysis (RSA), thus formally linking (fine scale) SSA with (broad scale) RSA. For the bank vole data, we show how our SSA-PDE approach can give predictions regarding the spatial aggregation and segregation of different individuals, which are difficult to predict purely by examining results of SSA. Our methods provide a user-friendly way into the world of PDEs, via a well-used statistical technique, which should lead to tighter links between the findings of mathematical ecology and observations from empirical ecology. By providing a non-speculative link between observed movement behaviours and space use patterns on larger spatio-temporal scales, our findings will also aid integration of movement ecology into understanding spatial species distributions.
Starch is the primary storage carbohydrate in most photosynthetic organisms and allows the accumulation of carbon and energy in form of an insoluble and semi-crystalline particle. In the last decades large progress, especially in the model plant Arabidopsis thaliana, was made in understanding the structure and metabolism of starch and its conjunction. The process underlying the initiation of starch granules remains obscure, although this is a fundamental process and seems to be strongly regulated, as in Arabidopsis leaves the starch granule number per chloroplast is fixed with 5-7. Several single, double, and triple mutants were reported in the last years that showed massively alterations in the starch granule number per chloroplast and allowed further insights in this important process. This mini review provides an overview of the current knowledge of processes involved in the initiation and formation of starch granules. We discuss the central role of starch synthase 4 and further proteins for starch genesis and affecting metabolic factors.
Starch is the primary storage carbohydrate in most photosynthetic organisms and allows the accumulation of carbon and energy in form of an insoluble and semi-crystalline particle. In the last decades large progress, especially in the model plant Arabidopsis thaliana, was made in understanding the structure and metabolism of starch and its conjunction. The process underlying the initiation of starch granules remains obscure, although this is a fundamental process and seems to be strongly regulated, as in Arabidopsis leaves the starch granule number per chloroplast is fixed with 5-7. Several single, double, and triple mutants were reported in the last years that showed massively alterations in the starch granule number per chloroplast and allowed further insights in this important process. This mini review provides an overview of the current knowledge of processes involved in the initiation and formation of starch granules. We discuss the central role of starch synthase 4 and further proteins for starch genesis and affecting metabolic factors.
A fluidic chip system was developed, which combines a stable generation of superoxide radicals and hydrogen peroxide with their sensorial detection. The generation of both reactive oxygen species was achieved by immobilization of xanthine oxidase on controlled pore glass in a reaction chamber. Antioxidants can be introduced into the fluidic chip system by means of mixing chamber. The detection of both species is based on the amperometric principle using a biosensor chip with two working electrodes. As sensing protein for both electrodes cytochrome c was used. The novel system was designed for the quantification of the antioxidant efficiency of different potential scavengers of the respective reactive species in an aqueous medium. Several model antioxidants such as ascorbic acid or catalase have been tested under flow conditions.
Background
Cells are able to communicate and coordinate their function within tissues via secreted factors. Aberrant secretion by cancer cells can modulate this intercellular communication, in particular in highly organised tissues such as the liver. Hepatocytes, the major cell type of the liver, secrete Dickkopf (Dkk), which inhibits Wnt/ β-catenin signalling in an autocrine and paracrine manner. Consequently, Dkk modulates the expression of Wnt/ β-catenin target genes. We present a mathematical model that describes the autocrine and paracrine regulation of hepatic gene expression by Dkk under wild-type conditions as well as in the presence of mutant cells.
Results
Our spatial model describes the competition of Dkk and Wnt at receptor level, intra-cellular Wnt/ β-catenin signalling, and the regulation of target gene expression for 21 individual hepatocytes. Autocrine and paracrine regulation is mediated through a feedback mechanism via Dkk and Dkk diffusion along the porto-central axis. Along this axis an APC concentration gradient is modelled as experimentally detected in liver. Simulations of mutant cells demonstrate that already a single mutant cell increases overall Dkk concentration. The influence of the mutant cell on gene expression of surrounding wild-type hepatocytes is limited in magnitude and restricted to hepatocytes in close proximity. To explore the underlying molecular mechanisms, we perform a comprehensive analysis of the model parameters such as diffusion coefficient, mutation strength and feedback strength.
Conclusions
Our simulations show that Dkk concentration is elevated in the presence of a mutant cell. However, the impact of these elevated Dkk levels on wild-type hepatocytes is confined in space and magnitude. The combination of inter- and intracellular processes, such as Dkk feedback, diffusion and Wnt/ β-catenin signal transduction, allow wild-type hepatocytes to largely maintain their gene expression.
The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.13 to 4.13 coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.73- and 5.33) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stableisotope analysis of this sample suggests a mixed terrestrial/ aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.
Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an similar to 5,000-year-old giant panda from Jiangdongshan, Teng-chong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions.
This cumulative habilitation thesis presents new work on the systematics, paleoecology, and evolution of antelopes and other large mammals, focusing mainly on the late Miocene to Pleistocene terrestrial fossil record of Africa and Arabia. The studies included here range from descriptions of new species to broad-scale analyses of diversification and community evolution in large mammals over millions of years. A uniting theme is the evolution, across both temporal and spatial scales, of the environments and faunas that characterize modern African savannas today. One conclusion of this work is that macroevolutionary changes in large mammals are best characterized at regional (subcontinental to continental) and long-term temporal scales. General views of evolution developed on records that are too restricted in spatial and temporal extent are likely to ascribe too much influence to local or short-lived events. While this distinction in the scale of analysis and interpretation may seem trivial, it is challenging to implement given the geographically and temporally uneven nature of the fossil record, and the difficulties of synthesizing spatially and temporally dispersed datasets. This work attempts to do just that, bringing together primary fossil discoveries from eastern Africa to Arabia, from the Miocene to the Pleistocene, and across a wide range of (mainly large mammal) taxa. The end result is support for hypotheses stressing the impact of both climatic and biotic factors on long-term faunal change, and a more geographically integrated view of evolution in the African fossil record.
Pace-of-life syndromes
(2018)
This introduction to the topical collection on Pace-of-life syndromes: a framework for the adaptive integration of behaviour, physiology, and life history provides an overview of conceptual, theoretical, methodological, and empirical progress in research on pace-of-life syndromes (POLSs) over the last decade. The topical collection has two main goals. First, we briefly describe the history of POLS research and provide a refined definition of POLS that is applicable to various key levels of variation (genetic, individual, population, species). Second, we summarise the main lessons learned from current POLS research included in this topical collection. Based on an assessment of the current state of the theoretical foundations and the empirical support of the POLS hypothesis, we propose (i) conceptual refinements of theory, particularly with respect to the role of ecology in the evolution of (sexual dimorphism in) POLS, and (ii) methodological and statistical approaches to the study of POLS at all major levels of variation. This topical collection further holds (iii) key empirical examples demonstrating how POLS structures may be studied in wild populations of (non) human animals, and (iv) a modelling paper predicting POLS under various ecological conditions. Future POLS research will profit from the development of more explicit theoretical models and stringent empirical tests of model assumptions and predictions, increased focus on how ecology shapes (sex-specific) POLS structures at multiple hierarchical levels, and the usage of appropriate statistical tests and study designs. Significance statement As an introduction to the topical collection, we summarise current conceptual, theoretical, methodological and empirical progress in research on pace-of-life syndromes (POLSs), a framework for the adaptive integration of behaviour, physiology and life history at multiple hierarchical levels of variation (genetic, individual, population, species). Mixed empirical support of POLSs, particularly at the within-species level, calls for an evaluation and refinement of the hypothesis. We provide a refined definition of POLSs facilitating testable predictions. Future research on POLSs will profit from the development of more explicit theoretical models and stringent empirical tests of model assumptions and predictions, increased focus on how ecology shapes (sex-specific) POLSs structures at multiple hierarchical levels and the usage of appropriate statistical tests and study designs.
As a tumor suppressor and the most frequently mutated gene in cancer, p53 is among the best-described molecules in medical research. As cancer is in most cases an age-related disease, it seems paradoxical that p53 is so strongly conserved from early multicellular organisms to humans. A function not directly related to tumor suppression, such as the regulation of metabolism in nontransformed cells, could explain this selective pressure. While this role of p53 in cellular metabolism is gradually emerging, it is imperative to dissect the tissue-and cell-specific actions of p53 and its downstream signaling pathways. In this review, we focus on studies reporting p53's impact on adipocyte development, function, and maintenance, as well as the causes and consequences of altered p53 levels in white and brown adipose tissue (AT) with respect to systemic energy homeostasis. While whole body p53 knockout mice gain less weight and fat mass under a high-fat diet owing to increased energy expenditure, modifying p53 expression specifically in adipocytes yields more refined insights: (1) p53 is a negative regulator of in vitro adipogenesis; (2) p53 levels in white AT are increased in diet-induced and genetic obesity mouse models and in obese humans; (3) functionally, elevated p53 in white AT increases senescence and chronic inflammation, aggravating systemic insulin resistance; (4) p53 is not required for normal development of brown AT; and (5) when p53 is activated in brown AT in mice fed a high-fat diet, it increases brown AT temperature and brown AT marker gene expression, thereby contributing to reduced fat mass accumulation. In addition, p53 is increasingly being recognized as crucial player in nutrient sensing pathways. Hence, despite existence of contradictory findings and a varying density of evidence, several functions of p53 in adipocytes and ATs have been emerging, positioning p53 as an essential regulatory hub in ATs. Future studies need to make use of more sophisticated in vivo model systems and should identify an AT-specific set of p53 target genes and downstream pathways upon different (nutrient) challenges to identify novel therapeutic targets to curb metabolic diseases
As a tumor suppressor and the most frequently mutated gene in cancer, p53 is among the best-described molecules in medical research. As cancer is in most cases an age-related disease, it seems paradoxical that p53 is so strongly conserved from early multicellular organisms to humans. A function not directly related to tumor suppression, such as the regulation of metabolism in nontransformed cells, could explain this selective pressure. While this role of p53 in cellular metabolism is gradually emerging, it is imperative to dissect the tissue-and cell-specific actions of p53 and its downstream signaling pathways. In this review, we focus on studies reporting p53's impact on adipocyte development, function, and maintenance, as well as the causes and consequences of altered p53 levels in white and brown adipose tissue (AT) with respect to systemic energy homeostasis. While whole body p53 knockout mice gain less weight and fat mass under a high-fat diet owing to increased energy expenditure, modifying p53 expression specifically in adipocytes yields more refined insights: (1) p53 is a negative regulator of in vitro adipogenesis; (2) p53 levels in white AT are increased in diet-induced and genetic obesity mouse models and in obese humans; (3) functionally, elevated p53 in white AT increases senescence and chronic inflammation, aggravating systemic insulin resistance; (4) p53 is not required for normal development of brown AT; and (5) when p53 is activated in brown AT in mice fed a high-fat diet, it increases brown AT temperature and brown AT marker gene expression, thereby contributing to reduced fat mass accumulation. In addition, p53 is increasingly being recognized as crucial player in nutrient sensing pathways. Hence, despite existence of contradictory findings and a varying density of evidence, several functions of p53 in adipocytes and ATs have been emerging, positioning p53 as an essential regulatory hub in ATs. Future studies need to make use of more sophisticated in vivo model systems and should identify an AT-specific set of p53 target genes and downstream pathways upon different (nutrient) challenges to identify novel therapeutic targets to curb metabolic diseases.
Lifestyle-related disorders, such as the metabolic syndrome, have become a primary risk factor for the development of liver pathologies that can progress from hepatic steatosis, hepatic insulin resistance, steatohepatitis, fibrosis and cirrhosis, to the most severe condition of hepatocellular carcinoma (HCC). While the prevalence of liver pathologies is steadily increasing in modern societies, there are currently no approved drugs other than chemotherapeutic intervention in late stage HCC. Hence, there is a pressing need to identify and investigate causative molecular pathways that can yield new therapeutic avenues. The transcription factor p53 is well established as a tumor suppressor and has recently been described as a central metabolic player both in physiological and pathological settings. Given that liver is a dynamic tissue with direct exposition to ingested nutrients, hepatic p53, by integrating cellular stress response, metabolism and cell cycle regulation, has emerged as an important regulator of liver homeostasis and dysfunction. The underlying evidence is reviewed herein, with a focus on clinical data and animal studies that highlight a direct influence of p53 activity on different stages of liver diseases. Based on current literature showing that activation of p53 signaling can either attenuate or fuel liver disease, we herein discuss the hypothesis that, while hyper-activation or loss of function can cause disease, moderate induction of hepatic p53 within physiological margins could be beneficial in the prevention and treatment of liver pathologies. Hence, stimuli that lead to a moderate and temporary p53 activation could present new therapeutic approaches through several entry points in the cascade from hepatic steatosis to HCC.
Oxidized protein aggregates
(2020)
The study of protein aggregates has a long history. While in the first decades until the 80ies of the 20th century only the observation of the presence of such aggregates was reported, later the biochemistry of the formation and the biological effects of theses aggregates were described.
This review focusses on the complexity of the biological effects of protein aggregates and its potential role in the aging process.
Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
Im Fokus dieser Arbeit stand der Aufbau einer auf DNA basierenden Nanostruktur. Der universelle Vier-Buchstaben-Code der DNA ermöglicht es, Bindungen auf molekularer Ebene zu adressieren. Die chemischen und physikalischen Eigenschaften der DNA prädestinieren dieses Makromolekül für den Einsatz und die Verwendung als Konstruktionselement zum Aufbau von Nanostrukturen. Das Ziel dieser Arbeit war das Aufspannen eines DNA-Stranges zwischen zwei Fixpunkten. Hierfür war es notwendig, eine Methode zu entwickeln, welche es ermöglicht, Funktionsmoleküle als Ankerelemente ortsaufgelöst auf eine Oberfläche zu deponieren. Das Deponieren dieser Moleküle sollte dabei im unteren Mikrometermaßstab erfolgen, um den Abmaßen der DNA und der angestrebten Nanostruktur gerecht zu werden. Das eigens für diese Aufgabe entwickelte Verfahren zum ortsaufgelösten Deponieren von Funktionsmolekülen nutzt das Bindungspaar Biotin-Neutravidin. Mit Hilfe eines Rasterkraftmikroskops (AFM) wurde eine zu einem „Stift“ umfunktionierte Rasterkraftmikroskopspitze so mit der zu deponierenden „Tinte“ beladen, dass das Absetzen von Neutravidin im unteren Mikrometermaßstab möglich war. Dieses Neutravidinmolekül übernahm die Funktion als Bindeglied zwischen der biotinylierten Glasoberfläche und dem eigentlichen Adressmolekül. Das somit generierte Neutravidin-Feld konnte dann mit einem biotinylierten Adressmolekül durch Inkubation funktionalisiert werden. Namensgebend für dieses Verfahren war die Möglichkeit, Neutravidin mehrmals zu deponieren und zu adressieren. Somit ließ sich sequenziell ein Mehrkomponenten-Feld aufbauen. Die Einschränkung, mit einem AFM nur eine Substanz deponieren zu können, wurde so umgangen. Ferner mußten Ankerelemente geschaffen werden, um die DNA an definierten Punkten immobilisieren zu können. Die Bearbeitung der DNA erfolgte mit molekularbiologischen Methoden und zielte darauf ab, einen DNA-Strang zu generieren, welcher an seinen beiden Enden komplementäre Adressequenzen enthält, um gezielt mit den oberflächenständigen Ankerelementen binden zu können. Entsprechend der Geometrie der mit dem AFM erzeugten Fixpunkte und den oligonukleotidvermittelten Adressen kommt es zur Ausbildung einer definierten DNA-Struktur. Mit Hilfe von fluoreszenzmikroskopischen Methoden wurde die aufgebaute DNA-Nanostruktur nachgewiesen. Der Nachweis der nanoskaligen Interaktion von DNA-bindenden Molekülen mit der generierten DNA-Struktur wurde durch die Bindung von PNA (peptide nucleic acid) an den DNA-Doppelstrang erbracht. Diese PNA-Bindung stellt ihrerseits ein funktionales Strukturelement im Nanometermaßstab dar und wird als Nanostrukturbaustein verstanden.
The organic-carbon (OC) pool accumulated in Arctic permafrost (perennially frozen ground) equals the carbon stored in the modern atmosphere. To give an idea of how Yedoma region permafrost could respond under future climatic warming, we conducted a study to quantify the organic-matter quality (here defined as the intrinsic potential to be further transformed, decomposed, and mineralized) of late Pleistocene (Yedoma) and Holocene (thermokarst) deposits on the Buor-Khaya Peninsula, northeast Siberia. The objective of this study was to develop a stratigraphic classified organic-matter quality characterization. For this purpose the degree of organic-matter decomposition was estimated by using a multiproxy approach. We applied sedimentological (grain-size analyses, bulk density, ice content) and geochemical parameters (total OC, stable carbon isotopes (delta C-13),total organic carbon : nitrogen (C / N) ratios) as well as lipid biomarkers (n-alkanes, n-fatty acids, hopanes, triterpenoids, and biomarker indices, i.e., average chain length, carbon preference index (CPI), and higher-plant fatty-acid index (HPFA)). Our results show that the Yedoma and thermokarst organic-matter qualities for further decomposition exhibit no obvious degradation-depth trend. Relatively, the C / N and delta C-13 values and the HPFA index show a significantly better preservation of the organic matter stored in thermokarst deposits compared to Yedoma deposits. The CPI data suggest less degradation of the organic matter from both deposits, with a higher value for Yedoma organic matter. As the interquartile ranges of the proxies mostly over-lap, we interpret this as indicating comparable quality for further decomposition for both kinds of deposits with likely better thermokarst organic-matter quality. Supported by principal component analyses, the sediment parameters and quality proxies of Yedoma and thermokarst deposits could not be unambiguously separated from each other. This revealed that the organic-matter vulnerability is heterogeneous and depends on different decomposition trajectories and the previous decomposition and preservation history. Elucidating this was one of the major new contributions of our multiproxy study. With the addition of biomarker data, it was possible to show that permafrost organic-matter degradation likely occurs via a combination of (uncompleted) degradation cycles or a cascade of degradation steps rather than as a linear function of age or sediment facies. We conclude that the amount of organic matter in the studied sediments is high for mineral soils and of good quality and therefore susceptible to future decomposition. The lack of depth trends shows that permafrost acts like a giant freezer, preserving the constant quality of ancient organic matter. When undecomposed Yedoma organic matter is mobilized via thermokarst processes, the fate of this carbon depends largely on the environmental conditions; the carbon could be preserved in an undecomposed state till refreezing occurs. If modern input has occurred, thermokarst organic matter could be of a better quality for future microbial decomposition than that found in Yedoma deposits.
The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.
Benthic microbial communities (BMCs) play important roles in the carbon cycle of lakes, and benthic littoral zones in particular have been previously highlighted as biogeochemical hotspots. Dissolved organic matter (DOM) presents the major carbon pool in lakes, and although the effect of DOM composition on the pelagic microbial community composition is widely accepted, little is known about its effect on BMCs, particularly aquatic fungi. Therefore, we investigated the composition of benthic littoral microbial communities in twenty highly diverse lakes in northeast Germany. DOM quality was analyzed via size exclusion chromatography (SEC), fluorescence parallel factor analyses (PRAFACs) and UV-Vis spectroscopy. We determined the BMC composition and biomass using phospholipid-derived fatty acids (PLFA) and extended the interpretation to the analysis of fungi by applying a Bayesian mixed model. We present evidence that the quality of DOM structures the BMCs, which are dominated by heterotrophic bacteria and show low fungal biomass. The fungal biomass increases when the DOM pool is processed by microorganisms of allochthonous origin, whereas the opposite is true for bacteria.
Organic matter characteristics in yedoma and thermokarst deposits on Baldwin Peninsula, west Alaska
(2018)
As Arctic warming continues and permafrost thaws, more soil and sedimentary organic matter (OM) will be decomposed in northern high latitudes. Still, uncertainties remain in the quality of the OM and the size of the organic carbon (OC) pools stored in different deposit types of permafrost landscapes. This study presents OM data from deep permafrost and lake deposits on the Baldwin Peninsula which is located in the southern portion of the continuous permafrost zone in west Alaska. Sediment samples from yedoma and drained thermokarst lake basin (DTLB) deposits as well as thermokarst lake sediments were analyzed for cryostratigraphical and biogeochemical parameters and their lipid biomarker composition to identify the below-ground OC pool size and OM quality of ice-rich permafrost on the Baldwin Peninsula. We provide the first detailed characterization of yedoma deposits on Baldwin Peninsula. We show that three-quarters of soil OC in the frozen deposits of the study region (total of 68 Mt) is stored in DTLB deposits (52 Mt) and one-quarter in the frozen yedoma deposits (16 Mt). The lake sediments contain a relatively small OC pool (4 Mt), but have the highest volumetric OC content (93 kgm(-3)) compared to the DTLB (35 kgm(-3)) and yedoma deposits (8 kgm(-3)), largely due to differences in the ground ice content. The biomarker analysis indicates that the OM in both yedoma and DTLB deposits is mainly of terrestrial origin. Nevertheless, the relatively high carbon preference index of plant leaf waxes in combination with a lack of a degradation trend with depth in the yedoma deposits indi-cates that OM stored in yedoma is less degraded than that stored in DTLB deposits. This suggests that OM in yedoma has a higher potential for decomposition upon thaw, despite the relatively small size of this pool. These findings show that the use of lipid biomarker analysis is valuable in the assessment of the potential future greenhouse gas emissions from thawing permafrost, especially because this area, close to the discontinuous permafrost boundary, is projected to thaw substantially within the 21st century.
OBJECTIVE:
Recent publications describing lingual movement strategies within the oral cavity of brass players have established the existence of efficient and predictable movement patterns in healthy performers for a variety of performance tasks. In this study we extend the research to include the playing of large interval slurs in horn players.
METHODS:
Real-time MRI films at 40-msec resolution were simultaneously obtained in the sagittal
and coronal planes in 9 professional horn players as they performed 2 repetitions each of 3 slur sequences spanning 1 octave, 1 octave + 3rd, and 1 octave + 5th at a mezzo forte dynamic level. Nine profile lines were overlaid on the images allowing the measurement of dorsal tongue edge movement using a customized MATLAB toolkit. Movement along lines representing the anterior, middle, and posterior oral cavity in the sagittal plane, as well as the vertical height of an air channel observed in the coronal plane, are reported.
RESULTS:
Both sagittal and coronal views demonstrate patterned tongue movements that narrow and widen the air channel during ascending and descending slurs, respectively. The magnitude of these movements is greater during larger intervals, though not perfectly consistent within each slur sequence. Additionally, the tongue position during notes
tends to drift in the direction of the subsequent note in each sequence. We suggest that the observed movements may help to modulate air speed through the lips, possible attenuating embouchure muscle tension changes by assisting changes in lip vibration frequency.
The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.
Die Enzymsuperfamilie der löslichen Sulfotransferasen (SULT) spielt eine wichtige Rolle in der Phase II des Fremdstoffmetabolismus. Sie katalysieren den Transfer einer Sulfonylgruppe auf nucleophile Gruppen endogener und exogener Substrate. Die Sulfokonjugation von Fremdstoffen erhöht deren Wasserlöslichkeit und behindert die passive Permeation von Zellmembranen. Dadurch wird die Ausscheidung dieser konjugierten Substanzen erleichtert. In Abhängigkeit von der Struktur des Zielmoleküls kann die Sulfokonjugation aber auch zur metabolischen Aktivierung von Fremdstoffen durch die Bildung instabiler Metabolite führen. Die SULT-vermittelte Aktivierung promutagener Substanzen ist somit von toxikologischem Interesse. Für die Detektion SULT-vermittelter Mutagenität mittels bakterieller in-vitro Testsysteme ist die heterologe Expression der fremdstoffmetabolisierenden Enzyme direkt in den Indikatorzellen notwendig. S. typhimurium exprimieren selbst keine SULT, und externe Metabolisierungssysteme sind problematisch, weil die negativ geladenen, kurzlebigen Metabolite nur schlecht die Zellmembran penetrieren können. Die Expression humaner Enyme in Bakterien ist jedoch zum Teil sehr kritisch. So zeigen z.B. sehr ähnliche Enzyme (SULT1A2*1 und *2) deutliche Unterschiede im Expressionsniveau bei exakt gleichen äußeren Bedingungen. Dies erschwert den Vergleich der enzymatischen Aktivitäten dieser Enzyme im in-vitro Testsystem. Andere Enzyme (z.B. SULT2B1b) werden unter Verwendung ihrer Wildtyp-cDNA zum Teil nicht detektierbar exprimiert. Deshalb sollte in dieser Arbeit eine Methode zur Optimierung der heterologen Expression fremdstoffmetabolisierender Enzyme für Genotoxizitätsuntersuchungen etabliert werden. Es wurde bereits gezeigt dass synonyme Codonaustausche am 5’-Ende der humanen SULT1A2-cDNA zu einer Erhöhung der Expression des entsprechenden Enzyms in S. typhimurium führten. Dementsprechend wurden in dieser Arbeit Codonaustausche am 5’-Ende der cDNA verschiedener SULT (1A1*1, 1A2*1, 2B1b) sowie der Ratten Glutathion-S-Transferase Theta 2 (rGSTT2) und dem Reportergen Luciferase durchgeführt. Die Expression der so generierten Konstrukte wurde in verschiedenen S. typhimurium und E. coli Stämmen quantifiziert und die Aktivität der überexprimierten Enzyme im Ames-Test bzw. im Enzym-Aktivitätsassay überprüft. Durch das Einführen seltener Codons in die cDNA konnte die Proteinexpression von SULT1A1*1, SULT1A2*1 und SULT2B1b maximal 7-fach, 18-fach und 100-fach im Vergleich zur Wildtyp-cDNA gesteigert werden. Die Expression der rGSTT2 wurde ebenfalls durch das Einführen seltener Codons erhöht (maximal 5-fach). Bei dem Reportergen Luciferase jedoch führte das Austauschen häufiger Codons gegen seltene Codons zu einer Reduktion der Proteinexpression um 80 %. Die Expression von Fusionsproteinen aus 2B1b (5’-Ende) und Luciferase (3’-Ende) wurde durch das Einführen seltener Codons ebenfalls um 50 % reduziert. Die S. typhimurium Stämme mit optimierter SULT 1A1*1- bzw. 1A2*1-Expression wurden im Ames-Test eingesetzt und zeigten im Vergleich zu den geringer exprimierenden Stämmen eine höhere Sensitivität. Für SULT2B1b konnte keine Mutagenaktivierung im Ames-Test nachgewiesen werden. Allerdings zeigte ein Enzym-Aktivitätsassay mit Dehydroepiandosteron, dass das bakteriell exprimierte Enzym funktionell war. Da in der Literatur der Effekt seltener Codons auf die Expression in Bakterien bisher fast ausschließlich als inhibitorisch beschrieben wurde, sollte die Wirkungsweise der hier beobachteten Expressionserhöhung durch seltene Codons genauer untersucht werden. Dazu wurden verschiedene Konstrukte der SULT1A2*1 und der SULT2B1b, die unterschiedlich viele seltene Codons in verschiedenen Kombinationen besaßen, hergestellt. Es konnten jedoch keine einzelnen Codons, die für die Expressionssteigerung allein verantwortlich waren, identifiziert werden. Die Plasmidkopienzahl in den verschiedenen SULT2B1b-Klonen war konstant und die SULT2B1b-mRNA-Konzentration zeigte nur moderate Schwankungen, die nicht als Ursache für die dramatische Erhöhung der SULT2B1b-Expression in Frage kommen. Die berechnete Stabilität der potentiellen mRNA-Sekundärstrukturen wurde durch die seltenen Codons häufig stark gesenkt und ist als eine mögliche Ursache für die Expressionssteigerung anzusehen. Zusätzlich erhöhten die seltenen Codons den Consensus der Downstream Box zur 16S rRNA, was ebenfalls eine Ursache für die Expressionssteigerung sein kann. In dieser Arbeit konnte somit die Expression der humanen SULT1A1*1, 1A2*1 und der 2B1b sowie der rGSTT2 erfolgreich mittels synonymer Codonaustausche erhöht werden. Die so optimierten S. typhimurium Stämme zeigten im Ames-Test eine erhöhte Sensitivität gegenüber SULT aktivierten Promutagenen bzw. erhöhte Aktivität in spezifischen Enymaktivitätsassays.
Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization.
Global Circulation Models of climate predict not only a change of annual precipitation amounts but also a shift in the daily distribution. To improve the understanding of the importance of daily rain pattern for annual plant communities, which represent a large portion of semi-natural vegetation in the Middle East, I used a detailed, spatially explicit model. The model explicitly considers water storage in the soil and has been parameterized and validated with data collected in field experiments in Israel and data from the literature. I manipulated daily rainfall variability by increasing the mean daily rain intensity on rainy days (MDI, rain volume/day) and decreasing intervals between rainy days while keeping the mean annual amount constant. In factorial combination, I also increased mean annual precipitation (MAP). I considered five climatic regions characterized by 100, 300, 450, 600, and 800 mm MAP. Increasing MDI decreased establishment when MAP was >250 mm but increased establishment at more arid sites. The negative effect of increasing MDI was compensated by increasing mortality with increasing MDI in dry and typical Mediterranean regions (c. 360–720 mm MAP). These effects were strongly tied to water availability in upper and lower soil layers and modified by competition among seedlings and adults. Increasing MAP generally increased water availability, establishment, and density. The order of magnitudes of MDI and MAP effects overlapped partially so that their combined effect is important for projections of climate change effects on annual vegetation. The effect size of MAP and MDI followed a sigmoid curve along the MAP gradient indicating that the semi-arid region (≈300 mm MAP) is the most sensitive to precipitation change with regard to annual communitie
The electric organ of the mormyrid weakly electric fish,Campylomormyrus rhynchophorus(Boulenger, 1898), undergoes changes in both the electric organ discharge (EOD) and the light and electron microscopic morphology as the fish mature from the juvenile to the adult form. Of particular interest was the appearance of papillae, surface specializations of the uninnervated anterior face of the electrocyte, which have been hypothesized to increase the duration of the EOD. In a 24.5 mm long juvenile the adult electric organ (EO) was not yet functional, and the electrocytes lacked papillae. A 40 mm long juvenile, which produced a short biphasic EOD of 1.3 ms duration, shows small papillae (average area 136 mu m(2)). In contrast, the EOD of a 79 mm long juvenile was triphasic. The large increase in duration of the EOD to 23.2 ms was accompanied by a small change in size of the papillae (average area 159 mu m(2)). Similarly, a 150 mm long adult produced a triphasic EOD of comparable duration to the younger stage (24.7 ms) but featured a prominent increase in size of the papillae (average area 402 mu m(2)). Thus, there was no linear correlation between EOD duration and papillary size. The most prominent ultrastructural change was at the level of the myofilaments, which regularly extended into the papillae, only in the oldest specimen-probably serving a supporting function. Physiological mechanisms, like gene expression levels, as demonstrated in someCampylomormyrusspecies, might be more important concerning the duration of the EOD.
The aim of this study was a longitudinal description of the ontogeny of the adult electric organ of Campylomormyrus rhynchophorus which produces as adult an electric organ discharge of very long duration (ca. 25 ms). We could indeed show (for the first time in a mormyrid fish) that the electric organ discharge which is first produced early during ontogeny in 33-mm-long juveniles is much shorter in duration and has a different shape than the electric organ discharge in 15-cm-long adults. The change from this juvenile electric organ discharges into the adult electric organ discharge takes at least a year. The increase in electric organ discharge duration could be causally linked to the development of surface evaginations, papillae, at the rostral face of the electrocyte which are recognizable for the first time in 65-mm-long juveniles and are most prominent at the periphery of the electrocyte.
Predation drives coexistence, evolution and population dynamics of species in food webs, and has strong impacts on related ecosystem functions (e.g. primary production). The effect of predation on these processes largely depends on the trade-offs between functional traits in the predator and prey community. Trade-offs between defence against predation and competitive ability, for example, allow for prey speciation and predator-mediated coexistence of prey species with different strategies (defended or competitive), which may stabilize the overall food web dynamics. While the importance of such trade-offs for coexistence is widely known, we lack an understanding and the empirical evidence of how the variety of differently shaped trade-offs at multiple trophic levels affect biodiversity, trait adaptation and biomass dynamics in food webs. Such mechanistic understanding is crucial for predictions and management decisions that aim to maintain biodiversity and the capability of communities to adapt to environmental change ensuring their persistence.
In this dissertation, after a general introduction to predator-prey interactions and tradeoffs, I first focus on trade-offs in the prey between qualitatively different types of defence (e.g. camouflage or escape behaviour) and their costs. I show that these different types lead to different patterns of predator-mediated coexistence and population dynamics, by using a simple predator-prey model. In a second step, I elaborate quantitative aspects of trade-offs and demonstrates that the shape of the trade-off curve in combination with trait-fitness relationships strongly affects competition among different prey types: Either specialized species with extreme trait combinations (undefended or completely defended) coexist, or a species with an intermediate defence level dominates. The developed theory on trade-off shapes and coexistence is kept general, allowing for applications apart from defence-competitiveness trade-offs. Thirdly, I tested the theory on trade-off shapes on a long-term field data set of phytoplankton from Lake Constance. The measured concave trade-off between defence and growth governs seasonal trait changes of phytoplankton in response to an altering grazing pressure by zooplankton, and affects the maintenance of trait variation in the community. In a fourth step, I analyse the interplay of different tradeoffs at multiple trophic levels with plankton data of Lake Constance and a corresponding tritrophic food web model. The results show that the trait and biomass dynamics of the different three trophic levels are interrelated in a trophic biomass-trait cascade, leading to unintuitive patterns of trait changes that are reversed in comparison to predictions from bitrophic systems. Finally, in the general discussion, I extract main ideas on trade-offs in multitrophic systems, develop a graphical theory on trade-off-based coexistence, discuss the interplay of intra- and interspecific trade-offs, and end with a management-oriented view on the results of the dissertation, describing how food webs may respond to future global changes, given their trade-offs.
Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.
Polymeric devices capable of releasing submicron particles (subMP) on demand are highly desirable for controlled release systems, sensors, and smart surfaces. Here, a temperature-memory polymer sheet with a programmable smooth surface served as matrix to embed and release polystyrene subMP controlled by particle size and temperature. subMPs embedding at 80 degrees C can be released sequentially according to their size (diameter D of 200 nm, 500 nm, 1 mu m) when heated. The differences in their embedding extent are determined by the various subMPs sizes and result in their distinct release temperatures. Microparticles of the same size (D approximate to 1 mu m) incorporated in films at different programming temperatures T-p (50, 65, and 80 degrees C) lead to a sequential release based on the temperature-memory effect. The change of apparent height over the film surface is quantified using atomic force microscopy and the realization of sequential release is proven by confocal laser scanning microscopy. The demonstration and quantification of on demand subMP release are of technological impact for assembly, particle sorting, and release technologies in microtechnology, catalysis, and controlled release.
Omics and male infertility
(2022)
Male infertility is a multifaceted disorder affecting approximately 50% of male partners in infertile couples.
Over the years, male infertility has been diagnosed mainly through semen analysis, hormone evaluations, medical records and physical examinations, which of course are fundamental, but yet inefficient, because 30% of male infertility cases remain idiopathic. This dilemmatic status of the unknown needs to be addressed with more sophisticated and result-driven technologies and/or techniques.
Genetic alterations have been linked with male infertility, thereby unveiling the practicality of investigating this disorder from the "omics" perspective.
Omics aims at analyzing the structure and functions of a whole constituent of a given biological function at different levels, including the molecular gene level (genomics), transcript level (transcriptomics), protein level (proteomics) and metabolites level (metabolomics). In the current study, an overview of the four branches of omics and their roles in male infertility are briefly discussed; the potential usefulness of assessing transcriptomic data to understand this pathology is also elucidated.
After assessing the publicly obtainable transcriptomic data for datasets on male infertility, a total of 1385 datasets were retrieved, of which 10 datasets met the inclusion criteria and were used for further analysis.
These datasets were classified into groups according to the disease or cause of male infertility.
The groups include non-obstructive azoospermia (NOA), obstructive azoospermia (OA), non-obstructive and obstructive azoospermia (NOA and OA), spermatogenic dysfunction, sperm dysfunction, and Y chromosome microdeletion.
Findings revealed that 8 genes (LDHC, PDHA2, TNP1, TNP2, ODF1, ODF2, SPINK2, PCDHB3) were commonly differentially expressed between all disease groups.
Likewise, 56 genes were common between NOA versus NOA and OA (ADAD1, BANF2, BCL2L14, C12orf50, C20orf173, C22orf23, C6orf99, C9orf131, C9orf24, CABS1, CAPZA3, CCDC187, CCDC54, CDKN3, CEP170, CFAP206, CRISP2, CT83, CXorf65, FAM209A, FAM71F1, FAM81B, GALNTL5, GTSF1, H1FNT, HEMGN, HMGB4, KIF2B, LDHC, LOC441601, LYZL2, ODF1, ODF2, PCDHB3, PDHA2, PGK2, PIH1D2, PLCZ1, PROCA1, RIMBP3, ROPN1L, SHCBP1L, SMCP, SPATA16, SPATA19, SPINK2, TEX33, TKTL2, TMCO2, TMCO5A, TNP1, TNP2, TSPAN16, TSSK1B, TTLL2, UBQLN3).
These genes, particularly the above-mentioned 8 genes, are involved in diverse biological processes such as germ cell development, spermatid development, spermatid differentiation, regulation of proteolysis, spermatogenesis and metabolic processes.
Owing to the stage-specific expression of these genes, any mal-expression can ultimately lead to male infertility.
Therefore, currently available data on all branches of omics relating to male fertility can be used to identify biomarkers for diagnosing male infertility, which can potentially help in unravelling some idiopathic cases.
Off-grid
(2018)
1. Advances in LED technology combined with solar, storable energy bring light to places remote from electricity grids. Worldwide more than 1.3 billion of people are living off-grid, often in developing regions of high insect biodiversity. In developed countries, dark refuges for wildlife are threatened by ornamental garden lights. Solar powered LEDs (SPLEDs) are cheaply available, dim, and often used to illuminate foot paths, but little is known on their effects on ground living (epigeal) arthropods.
2. We used off-the-shelf garden lamps with a single ‘white’ LED (colour temperature 7250 K) to experimentally investigate effects on attraction and nocturnal activity of ground beetles (Carabidae).
3. We found two disparate and species-specific effects of SPLEDs. (i) Some nocturnal, phototactic species were not reducing activity under illumination and were strongly attracted to lamps (>20-fold increase in captures compared to dark controls). Such species aggregate in lit areas and SPLEDs may become ecological traps, while the species is drawn from nearby, unlit assemblages. (ii) Other nocturnal species were reducing mobility and activity under illumination without being attracted to light, which may cause fitness reduction in lit areas.
4. Both reactions offer mechanistic explanations on how outdoor illumination can change population densities of specific predatory arthropods, which may have cascading effects on epigeal arthropod assemblages. The technology may thus increase the area of artificial light at night (ALAN) impacting insect biodiversity.
5. Measures are needed to mitigate effects, such as adjustment of light colour temperature and automated switch-offs.