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Humanity is constantly confronted with the emergence and reemergence of infectious diseases. Many of them produce large or devastating epidemics, like AIDS (HIV) and Ebola. Others have been long neglected, yet pose immediate threats to global public health as evidences the abrupt emergence of Zika virus in South America and its association with microcephaly in babies. The examples illustrate, that many of these diseases are provoked by RNA viruses. One of the first steps in understanding and eliminating those threats is the development of sensitive and rapid diagnostic methods. A general and relatively rapid method is the direct detection and examination of the agent’s genome. However, the nature of (re)emerging RNA viruses poses a series of very specific problems for the design of such methods. Therefore, a systematic approach was proposed for the design of DNA-hybridization-base methods to detect and characterize RNA viruses that will have both a high sensitivity and a specificity sufficiently broad to detect, per reaction, down to a single copy of any of the possible variants of the viral genome.
Following this approach a series of assays were designed, developed or adapted and put into use for detection and characterization of important RNA viruses. One of those viruses is West Nile virus (WNV), which after its explosive introduction into USA become the most widespread flavivirus throughout the world and, consequently, many countries began an intensive monitoring. While existing assay detected predominantly the Lineage 1, in Europa Lineage 2 was expected. Two new RT-qPCR for the detection of both lineages were developed, and reportedly used by independent laboratories. Due to more than 50000 associated deaths per year, the Hepatitis E virus also received an increasing attention to elucidate novel routes of transmission. This virus (especially genotype 3) has the zoonotic potential of transmission from pigs and wild boar to humans. RT-qPCR and nested qPCR for detection and characterization of this virus as well as a methodology for subtyping were developed and the first detected case of subtype 3b in a German wild animal was documented. In addition a novel assay for flaviviruses conformed by a RT-qPCR coupled with a low density DNA microarray was developed, which enabled the identification of WNV in mosquitoes from Greece. A RT-qPCR suitable for surveillance and diagnostic of all known variants of Venezuelan equine encephalitis virus was developed too. A causative agent of hemorrhagic infections, the Ngari virus, was detected and characterized in animal samples from Mauritania. These achievements were supported by the development of software applications for selection and visualization of primers and probes from aligned DNA sequences and for modeling of DNA hybridizations using unaligned sequences.
In conclusion a general methodology for rapid development of sensitive diagnostic methods based in DNA-hybridization technics (PCR, sequencing and microarray) was stablished and successful applications are reported.
There is an increasingly urgent need to understand and predict how organisms will cope with the environmental consequences of global climate change. Adaptation in any form can be mediated by genetic adaptation and/or by phenotypic plasticity. Disentangling these two adaptive processes is critical in understanding and predicting adaptive responses to environmental change. Usually, disentangling genetic adaptation from phenotypic plasticity requires common garden experiments conducted under controlled laboratory conditions. While these experiments are powerful, it is often difficult to translate the results into natural populations and extrapolate to naturally occurring phenotypic variation. One solution to this problem is provided by the many examples of invasive species that exhibit wide phenotypic variation and that reproduce asexually. Besides selecting the appropriate in situ model, one must carefully choose a relevant trait to investigate. Ecomorphology has been a central theme in evolutionary biology because it reflects how organisms can adapt to their environment through their morphology. Intraspecific ecomorphological studies are especially well suited to identify adaptive pressures and provide insights into the microevolutionary mechanisms leading to the phenotypic differentiation.
One excellent candidate for an intraspecific ecomorphological study aiming to understand adaptation through genetic adaptation and phenotypic plasticity is the invasive New Zealand mudsnail Potamopyrgus antipodarum Gray (1853). This ovoviviparous snail features high variability in shell morphology and has successfully invaded a wide range of fresh- and brackish water habitats around the world. The evolutionary and ecological situations in this species’ native and invasive ranges is drastically different. In New Zealand, P. antipodarum’s native range, sexual and asexual individuals coexist and experience selective pressure by sterilizing endoparasites. By contrast, only a few asexual lineages have been established in invaded regions around the globe, where parasite infection is extremely rare. Here, we took advantage of the low genetic diversity among asexually reproducing European individuals in an attempt to characterize the relative contribution of genetic variation and phenotypic plasticity to the wide variation in shell morphology of this snail.
Analysing the ecomorphology of 425 European P. antipodarum in a geometric-morphometric framework, using brood size as proxy for fecundity, and mtDNA and nuclear SNPs to account for relatedness and identify reproductive mode, we hypothesized that 1) shell variation in the invasive range should be adaptive with respect to colonization of novel habitats, and 2) at least some of the variation might be caused by phenotypic plasticity. We then expanded our ecomorphological scope by analysing 996 native specimens, expecting 1) genetic and morphological diversity to be higher in the native range compared to invaded regions; 2) morphological diversity to be higher in sexual compared to asexual individuals according to the frozen niche hypothesis; and 3) shell morphology to be habitat specific, hence adaptative. In a last part, we used computational fluid dynamics simulations to calculate relative drag and lift forces of three shell morphologies (globular, intermediate, and slender). Here, we tested the overall hypothesis that shell morphology in gastropods is an adaptation against dislodgement through lift rather than drag forces, which would explain the counterintuitive presence of wider shells with shorter spires in lotic environments. With a final flow tank experiment, we tested the specific hypothesis that the dislocation velocity of living snails is positively linked to foot size, and that the latter can be predicted by shell morphology, in particular the aperture area as assumed by several authors.
As expected, we found genetic and morphological diversity to be higher in native than in invasive snails, but surprisingly no higher morphological diversity in sexual versus asexual individuals. The relationships between shell morphology, habitat, and fecundity were complex. Shape variation was primarily linked to genetic relatedness, but specific environmental factors including flow rate induced similar shell shapes. By contrast, shell size was largely explained by environmental factors. Fecundity was correlated with size, but showed trade-offs with shape in increasingly extreme conditions. With increasing flow and in smaller habitats such as springs, the trend of shell shape becoming wider was reversed, i.e. snails with slender shells were brooding more embryos. This increase in fitness was explained by our CFD simulations: in lotic habitats, slender shells experience less drag and lift forces compared to globular shells. We found no correlation between foot size and shell shape or aperture area showing that the assumed aperture/foot area correlation should be used with caution and cannot be generalized for all aquatic gastropod species. Finally, shell morphology and foot size were not related to dislodgement speed in our flow tank experiment. We concluded that the relationship of shell morphology and flow velocity is more complex than assumed. Hence, other traits must play a major role in decreasing dislodgement risk in stream gastropods, e.g. specific behaviours or pedal mucus stickiness. Although we did not find that globular shells are adaptations decreasing dislodgement risk, we cannot rule out that they are still flow related adaptations. For instance, globular shells are more crush-resistant and might therefore represent a flow adaptation in terms of diminishing damage caused by tumbling after dislodgement or against lotic specific crush-type predators.
At this point, we can conclude that shell morphology in P. antipodarum varies at least in part as an adaptation to specific environmental factors. This study shows how essential it is to reveal how plastic, genetically as well as phenotypically, adaptive traits in species can be and to identify the causal factors and how these adaptations affect the fitness in order to better predict how organisms will cope with changing environmental conditions.
Recent research suggests that the P3b may be closely related to the activation of the locus coeruleus-norepinephrine (LC-NE) system. To further study the potential association, we applied a novel technique, the non-invasive transcutaneous vagus nerve stimulation (tVNS), which is speculated to increase noradrenaline levels. Using a within-subject cross-over design, 20 healthy participants received continuous tVNS and sham stimulation on two consecutive days (stimulation counterbalanced across participants) while performing a visual oddball task. During stimulation, oval non-targets (standard), normal-head (easy) and rotated-head (difficult) targets, as well as novel stimuli (scenes) were presented. As an indirect marker of noradrenergic activation we also collected salivary alpha-amylase (sAA) before and after stimulation. Results showed larger P3b amplitudes for target, relative to standard stimuli, irrespective of stimulation condition. Exploratory post hoc analyses, however, revealed that, in comparison to standard stimuli, easy (but not difficult) targets produced larger P3b (but not P3a) amplitudes during active tVNS, compared to sham stimulation. For sAA levels, although main analyses did not show differential effects of stimulation, direct testing revealed that tVNS (but not sham stimulation) increased sAA levels after stimulation. Additionally, larger differences between tVNS and sham stimulation in P3b magnitudes for easy targets were associated with larger increase in sAA levels after tVNS, but not after sham stimulation. Despite preliminary evidence for a modulatory influence of tVNS on the P3b, which may be partly mediated by activation of the noradrenergic system, additional research in this field is clearly warranted. Future studies need to clarify whether tVNS also facilitates other processes, such as learning and memory, and whether tVNS can be used as therapeutic tool.
Aquaporins (AQPs) facilitate the transepithelial water flow involved in epithelial fluid secretion in numerous tissues; however, their function in the pancreas is less characterized. Acute pancreatitis (AP) is a serious disorder in which specific treatment is still not possible. Accumulating evidence indicate that decreased pancreatic ductal fluid secretion plays an essential role in AP; therefore, the aim of this study was to investigate the physiological and pathophysiological role of AQPs in the pancreas. Expression and localization of AQPs were investigated by real-time PCR and immunocytochemistry, whereas osmotic transmembrane water permeability was estimated by the dye dilution technique, in Capan-1 cells. The presence of AQP1 and CFTR in the mice and human pancreas were investigated by immunohistochemistry. Pancreatic ductal HCO3- and fluid secretion were studied on pancreatic ducts isolated from wild-type (WT) and AQP1 knock out (KO) mice using microfluorometry and videomicroscopy, respectively. In vivo pancreatic fluid secretion was estimated by magnetic resonance imaging. AP was induced by intraperitoneal injection of cerulein and disease severity was assessed by measuring biochemical and histological parameters. In the mice, the presence of AQP1 was detected throughout the whole plasma membrane of the ductal cells and its expression highly depends on the presence of CFTR Cl- channel. In contrast, the expression of AQP1 is mainly localized to the apical membrane of ductal cells in the human pancreas. Bile acid treatment dose- and time-dependently decreased mRNA and protein expression of AQP1 and reduced expression of this channel was also demonstrated in patients suffering from acute and chronic pancreatitis. HCO3- and fluid secretion significantly decreased in AQP1 KO versus WT mice and the absence of AQP1 also worsened the severity of pancreatitis. Our results suggest that AQP1 plays an essential role in pancreatic ductal fluid and HCO3- secretion and decreased expression of the channel alters fluid secretion which probably contribute to increased susceptibility of the pancreas to inflammation.
Herpesviruses are a fascinating group of enveloped DNA viruses, which rely on membrane fusion for infectious entry and direct cell-to-cell spread. Compared with many other enveloped viruses, they utilize a remarkably complex fusion machinery. Three conserved virion proteins, the bona fide fusion protein gB, and the presumably gB activating gH/gL heterodimer constitute the conserved core fusion machinery and are believed to drive membrane fusion in a cascade-like fashion. Activation of this cascade in most alphaherpesviruses is proposed to be triggered by binding of gD to specific host cell receptors. The molecular details of this fusion process, however, remain largely elusive. Yet, a detailed mechanistic knowledge of this process would be greatly beneficial for the development of efficient countermeasures against a variety of diseases. In this thesis, the functional relevance of individual components of the essential gH/gL complex of the alphaherpesvirus PrV has been assessed by two different approaches: by reversion analysis (paper II) and site-directed mutagenesis (papers III-V). In contrast to other herpesviruses, gL-deleted PrV is able to perform limited cell-to-cell spread, providing the unique opportunity to passage the entry-deficient virus in cell culture to select for PrV revertants capable of infecting cells gL-independently. This approach already resulted in an infectious gL-negative PrV mutant (PrV-ΔgLPass), in which the function of gL was compensated by formation of a gDgH hybrid protein. Here, the requirements for gL-independent infectivity of a second independent revertant (PrV-ΔgLPassB4.1), were analyzed. Sequencing of the genes encoding for gB, gH and gD, revealed mutations in each of them. By means of a robust infection-free, transfection-based cell-cell fusion assay (paper I), we identified two amino acid substitutions in the gL-binding domain I of gHB4.1 (L70P, W103R) as sufficient to compensate for lack of gL. Two mutations in gB (G672R, ΔK883) were found to enhance fusogenicity, probably by lowering the energy, required for gB refolding from pre- to postfusion conformation. Coexpression of gHB4.1 and gBB4.1 led to an excess fusion, which was completely suppressed by gDB4.1 in the fusion assays. This was surprising since PrV gD is normally not required for in vitro fusion or direct viral cell-to-cell spread, clearly separating this process from fusion during entry, for which PrV gD is essential. The fusion inhibiting effect of gDB4.1 could be attributed to a single point mutation resulting in an amino acid substitution within the ectodomain (A106V). In conclusion, these results indicated that gL is not central to the fusion process, as its function can be compensated for. As found so far, gL-independent infectivity can be realized by compensatory mutations in gH (as in PrV-ΔgLPass) or in gH plus gB (as in PrV-ΔgLPassB4.1). Excessive fusion induced by gHB4.1 and gBB4.1 was counter-regulated by gDB4.1, indicating that the interplay between these proteins is precisely regulated and further implies that gL and gD, despite being not absolutely essential for the fusion process, have important regulatory functions on gH and/or gB.
Both PrV-ΔgLPass mutants had acquired compensatory mutations in gH affecting the predicted gL-binding domain I in gH. By construction of an artificial gH32/98, which lacked the predicted gL-binding domain and was similar to the recently crystallized gH-core fragment present in the gDgH hybrid protein, we identified the N-terminal part of PrV gH as essential for gH function during fusion (paper III). gH32/98 was unable to promote fusion of wild-type gB in fusion assays and led to a total loss of function in the viral context. These results indicated that the gD moiety, present in gDgH, is critical for proper function of the gH-core fragment. We hypothesize that the gD moiety may adopt a stabilizing or modulating influence on the gH structure, which is normally executed by gL and important for interaction of gH with wild-type gB. Remarkably, substitution of wild-type gB by gBB4.1 rescued function of gH32/98 in the cellular and viral contexts. These findings suggest that gBB4.1 has been selected for interaction with “gL-less” gH. In conclusion, these results demonstrated that gL and the gL-binding domain are not strictly required for membrane fusion during virus entry and spread but that compensatory mutations must be present in gB to restore a fully functional fusion machinery. These results strongly support the notion of a functional gH-gB interaction as a prerequisite for membrane fusion.
In addition to the N-terminal domain, we identified the transmembrane domain of PrV gH as an essential component of the fusion machinery, while the cytoplasmic domain was demonstrated to play a modulatory but nonessential role (paper IV). Whereas truncation or substitution of the PrV gH TMD by a gpi-anchor or the analogous sequence from PrV gD rendered gH non-functional, the HSV-1 gH TMD was found to functionally substitute for the PrV gH TMD in cell-cell fusion and complementation assays. Since residues in the TMD which are conserved between HSV and PrV gH but absent in PrV gD, are placed on one face of an α-helical wheel plot, we hypothesize that the gH TMD has an intrinsic property to interact with membrane components such as lipids or other molecules as a requirement for promoting membrane fusion.
In a final study focusing on the function of gH, we identified the N-glycosylation sites utilized by PrV gH, and determined their individual role in viral infection (paper V). PrV gH was found to be modified by N-glycans at five potential glycosylation sites. N-glycans at PrV specific N77 and the highly conserved site N627 were found to be critical for efficient membrane fusion in the fusion assays, and during viral entry and cell-to-cell spread. N627 was further shown to be crucial for proper gH transport and maturation. In contrast, inactivation of N604, conserved in the Varicellovirus genus, enhanced in vitro fusion activity and viral cell-to-cell spread. These findings demonstrated a role of the N-glycans in proper localization and function of PrV gH.
Individual white spruce (Picea glauca (Moench) Voss) growth limitations at treelines in Alaska
(2018)
White spruce (Picea glauca (Moench) Voss) is one of the most common conifers in Alaska and various treelines mark the species distribution range. Because treelines positions are driven by climate and because climate change is estimated to be strongest in northern latitudes, treeline shifts appear likely. However, species range shifts depend on various species parameters, probably most importantly on phenotypic plasticity, genetic adaptation
and dispersal. Due to their long generation cycles and their immobility, trees evolved to endure a wide variety of climatic conditions. In most locations, interannual climate variability is larger than the expected climate change until 2100. Thus treeline position is typically thought of as the integrated effect of multiple years and to lag behind gradual climate change by several decades. Past dendrochronological studies revealed that growth of white spruce in Alaska can be limited by several climatic variables, in particular water stress and low temperatures. Depending on how the intensity of climate warming, this could result in a leading range edge at treelines limited by low temperatures and trailing treelines where soil moisture is or becomes most limiting. Climate-growth correlations are the dendrochronological version of reaction norms and describe the relationship between an environmental variable and traits like tree-ring parameters (e.g. ring width, wood density, wood anatomy). These correlations can be used to explore potential effects of climate change on a target species. However, it is known that individuals differ with respect to multiple variables like size, age, microsite conditions, competition status or their genome. Such individual differences could be important because they can modulate climate-growth relationships and consequently also range shifts and growth trends. Removing individual differences by averaging tree-ring parameters of many individuals into site chronologies could be an oversimplification that might bias estimates of future white spruce performance. Population dynamics that emerge from the interactions of individuals (e.g. competition) and the range of reactions to the same environmental drivers can only be studied via individual tree analyses. Consequently, this thesis focuses on factors that might alter individual white spruce’ climate sensitivity and methods to assess such effects. In particular, the research articles included explore three topics:
1. First, clones were identified via microsatellites and high-frequency climate signals of clones were compared to that of non-clonal individuals. Clonal and non-clonal individuals showed similar high-frequency climate signals which allows to use clonal and non-clonal individuals to construct mean site chronologies. However, clones were more frequently found under the harsher environmental conditions at the treelines which could be of interest for the species survival strategy at alpine treelines and is further explored in the associated RESPONSE project A5 by David Würth.
2. In the second article, methods for the exploration and visualization of individual-tree differences in climate sensitivity are described. These methods represent a toolbox to explore causes for the variety of different climate sensitivities found in individual
trees at the same site. Though, overlaying gradients of multiple factors like temperature, tree density and/or tree height can make it difficult to attribute a single cause to the range of reaction norms (climate growth correlations).
3. Lastly, the third article attempts to disentangle the effect of age and size on climate-growth correlations. Multiple past studies found that trees of different Ages responded differently to climatic drivers. In contrast, other studies found that trees do not age like many other organisms. Age and size of a trees are roughly correlated, though there are large differences in the growth rate of trees, which can lead to smaller trees that are older than taller trees. Consequently, age is an imperfect Proxy for size and in contrast to age, size has been shown to affect wood anatomy and thus tree physiology. The article compares two tree-age methods and one tree-size method based on cumulative ring width. In line with previous research on aging and Wood anatomy, tree size appeared to be the best predictor to explain ontogenetic changes in white spruce’ climate sensitivity. In particular, tallest trees exhibited strongest correlations with water stress in previous year July. In conclusion, this thesis is about factors that can alter climate-growth relationships (reaction norms) of white spruce. The results emphasize that interactions between climate variables and other factors like tree size or competition status are important for estimates of future tree growth and potential treeline shifts. In line with previous studies on white spruce in Alaska, the results of this thesis underline the importance of water stress for white spruce.
Individuals that are taller and that have more competitors for water appear to be most susceptible to the potentially drier future climate in Alaska. While tree ring based growth trends estimates of white spruce are difficult to derive due to multiple overlaying low frequency (>10 years) signals, all investigated treeline sites showed highest growth at the treeline edge. This could indicate expanding range edges. However, a potential bottleneck for treeline advances and retreats could be seedling establishment, which should be explored in more detail in the future.