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Die Einschleppung gebietsfremder Parasiten durch den Menschen ist einer der Hauptgründe für das Auftreten neuer Krankheiten in the letzten Jahrzehnten. Neue Wirte sind oftmals anfälliger für diese invasiven Parasiten als die ursprünglichen Wirte. In schwerwiegenden Fällen können invasive Parasiten zu Massensterben und zum Aussterben ihrer neuen Wirte führen. Der ursprüngliche Wirt des Aalparasiten Anguillicola crassus ist der Japanische Aal. In den frühen 1980er Jahren wurde der Parasit in die Population des Europäischen Aals eingeschleppt. Er ist einer der Faktoren, die für den Populationsrückgang des Europäischen Aals verantwortlich sind. Die molekularen Prozesse, die zur stärkeren Anfälligkeit des Europäischen Aals im Vergleich zum Japanischen Aal führen, sind noch nicht zureichend bekannt. Die Analyse transkriptomweiter differenzieller Genexpression von Immungewebe ergab, dass im Europäischen Aal sowohl Immun- als auch Nichtimmungene differenziell exprimiert waren. Dies war im Japanischen Aal nicht der Fall und deutet darauf hin, dass der Europäische Aal eine ineffiziente und kostspielige Immunantwort auslöst. Die Resultate ensprechen jenen die schon in anderen Wirbeltierwirt-invasiven Parasiten-Systemen beobachtet wurden. Ausserdem stützen diese Resultate die Hypothese, dass neuen Wirten eine wirksame Immunantwort fehlt und sie deuten darauf hin, dass Nichtimmunprozesse wesentlich zur höheren Anfälligkeit von neuen Wirten beitragen. Als Reaktion of die negativen Fitnesseffekte können neue Wirte Abwehrmechanismen entwickeln. Im Europäischen Aal entspricht das der Einkapselung von A. crassus. Einkapselung führte zu eine niedrigere Abundanz adulter A. crassus. Dies deutet darauf hin, dass das Einkapseln sich positiv auf die Gesundheit infizierter Aale auswirkt. Jedoch war die Abundanz zweier nativer Parasiten höher in Aalen, die A. crassus einkapselten. Eine verbesserte Abwehr des eingeschleppten Parasiten könnte daher die Abwehr nativer Parasiten beeinträchtigen. / The human-mediated translocation of non-native parasites into foreign regions is one of the primary factors for the emergence of new diseases in recent decades. Novel hosts are often more susceptible to these invasive parasites than the native host. In severe cases, invasive parasites can lead to population declines and extinctions of their novel hosts. The eel parasite Anguillicola crassus is native to the Japanese eel. In the early 1980s it was introduced into the European eel population and is now considered to be one factor contributing to the population decline of its novel host. The underlying molecular processes determining higher susceptibility in the European eel compared to the Japanese eel are not well understood. Using whole-transcriptome differential gene expression analysis of immune organs, I found that genes involved in both immune and non-immune processes were differentially expressed in the European eel but not the Japanese eel, suggestive of an ineffective and costly immune response in the former. These results are in line with those observed between susceptible and resistant hosts in other vertebrate host-invasive parasite systems. Furthermore, the results support the hypothesis that novel hosts lack an effective immune response. The results also suggest that alteration of non-immune processes contributes substantially higher susceptibilities of novel hosts. In response to the negative fitness effects of invasive parasites, novel hosts can evolve coping mechanisms. The European eel has the capacity to encapsulate and kill A. crassus. Using natural infections, I found a lower abundance of adult A. crassus, the most costly parasitic stage in those eels encapsulating the parasite, suggesting that encapsulation can potentially improve health of infected eels. At the same time, the abundance of two native parasites was higher in those eels encapsulating A. crassus. Thus, coping with A. crassus may come at the expense of coping with native parasites.

Applicable image-based reconstruction of three-dimensional (3D) objects offers many interesting industrial as well as private use cases, such as augmented reality, reverse engineering, 3D printing and simulation tasks. Unfortunately, image-based 3D reconstruction is not yet applicable to these quite complex tasks, since the resulting 3D models are single, monolithic objects without any division into logical or functional subparts. This thesis aims at making image-based 3D reconstruction feasible such that captures of standard cameras can be used for creating functional 3D models. The research presented in the following does not focus on the fine-tuning of algorithms to achieve minor improvements, but evaluates the entire processing pipeline of image-based 3D reconstruction and tries to contribute at four critical points, where significant improvement can be achieved by advanced human-computer interaction: (i) As the starting point of any 3D reconstruction process, the object of interest (OOI) that should be reconstructed needs to be annotated. For this task, novel pixel-accurate OOI annotation as an interactive process is presented, and an appropriate software solution is released. (ii) To improve the interactive annotation process, traditional interface devices, like mouse and keyboard, are supplemented with human sensory data to achieve closer user interaction. (iii) In practice, a major obstacle is the so far missing standard for file formats for annotation, which leads to numerous proprietary solutions. Therefore, a uniform standard file format is implemented and used for prototyping the first gaze-improved computer vision algorithms. As a sideline of this research, analogies between the close interaction of humans and computer vision systems and 3D perception are identified and evaluated. (iv) Finally, to reduce the processing time of the underlying algorithms used for 3D reconstruction, the ability of artificial neural networks to reconstruct 3D models of unknown OOIs is investigated. Summarizing, the gained improvements show that applicable image-based 3D reconstruction is within reach but nowadays only feasible by supporting human-computer interaction. Two software solutions, one for visual video analytics and one for spare part reconstruction are implemented. In the future, automated 3D reconstruction that produces functional 3D models can be reached only when algorithms become capable of acquiring semantic knowledge. Until then, the world knowledge provided to the 3D reconstruction pipeline by human computer interaction is indispensable.

Umweltveränderungen durch natürliche und/oder menschliche Einflüsse (insbesondere der Verlust und die Fragmentierung von Lebensraum) sind wichtige Faktoren, die zum weltweiten Artenschwund beitragen. Einer der entscheidendsten Beiträge zum weltweiten Rückgang der biologischen Vielfalt, ist der kommerzielle Holzeinschlag. Insbesondere in tropischen Regenwäldern, etwa in Westafrika, ist dies besonders besorgniserregend, da wenig untersuchte, diverse Wirbeltiergemeinschaften von einem starken kommerziellen Holzeinschlag betroffen sind. Frühere Studien haben bereits die negativen Auswirkungen großflächiger Abholzung auf die taxonomische und funktionale Vielfalt von Amphibiengemeinschaften, aber auch auf die Gesundheit von Individuen identifiziert. Umweltveränderungen können sich also auch nachteilig auf eine Wirts- Parasit-Beziehung auswirken, was nicht zuletzt zu einer verringerten Überlebensfähigkeit der Wirtsarten führen kann. Die Untersuchung der Auswirkungen von Störungen Abholzung und Umweltveränderungen auf Amphibien, sowie auf bestehende Wirts-Parasiten-Beziehungen sind daher von größter Bedeutung um nachhaltige Waldwirtschaft und zukünftige Naturschutzmaßnahmen planen zu können. In dieser Arbeit möchte ich mittels eines Regenerationsgradienten nach einer Störung (Abholzung) untersuchen, wie sich die Dynamik einer Amphibiengemeinschaft verschiebt und wie diese Störung die Wirts-Parasit-Beziehung beeinflusst. Ich verwende einen kombinierten Datensatz (Amphibie [Wirt], Milbe [Parasit] und Umweltbedingungen [Habitat]) der über zwei Zeiträumen im Abstand von 15 Jahren (1999-2000 und 2016-2017) an identischen Standorten (vor 45 Jahren abgeholzter Wald und Primärwald) im Taï-Nationalpark (TNP) in der Elfenbeinküste gesammelt wurde, um die Anpassungsfähigkeit von Fröschen und ihren Parasiten an sich ändernde Umgebungen zu untersuchen. In einem ersten Artikel unterstreiche ich die Bedeutung auch kleiner Waldgebiete als potenzielle Quellen für unbeschriebene Biodiversität. In einem kleinen, nie zuvor untersuchten Sumpfwald in der südöstlichen Elfenbeinküste fand ich eine neue Blattstreufroschart der Gattung Phrynobatrachus. Anhand charakteristischer morphologischer Merkmale, einer beträchtlichen, molekulargenetischen Distanz zu anderen westafrikanischen Phrynobatrachus-Arten, sowie eines individuellen, männlichen Anzeigerufes beschreibe ich Phrynobatrachus tanoeensis sp. nov. als eine für die Wissenschaft neue Art. Im zweiten Artikel untersuche ich die Widerstandsfähigkeit westafrikanischer Frösche in Wäldern, die vor über 45 Jahren selektiv abgeholzt wurden. Ich vergleiche die Diversität, Abundanz, Zusammensetzung und den Lebensraum von Amphibiengemeinschaften in abgeholzten und Primärwäldern innerhalt zweier Zeiträume (2000 und 2016- 2017). Ich konnte herausarbeiten, dass sich die Struktur des zuvor abgeholzten Waldes im Laufe von 45 Jahren langsam der des Primärwaldes annäherte, wobei die sichtbarsten Veränderungen in den letzten 15 Jahren auftraten. Während ich 30 Jahre nach dem Holzeinschlag zwar keine Unterscheide mehr in der Diversität und Abundanz der Amphibiengemeinschaft zum Primärwald feststellen konnte, beobachtete ich jedoch eine fortschreitende Konvergenz der Zusammensetzung der Amphibiengesellschaften in beiden Waldtypen. In den zuvor abgeholzten Wäldern erholten sich mehrere waldspezialisierte Arten (FS), während die Zahl mehrerer Generalisten (FG) über den 15-jährigen Probenahmezeitraum stetig abnahm. Diese Ergebnisse deuten darauf hin, dass 45 Jahre nach der Abholzung der gestörte Lebensraum allmählich die Heterogenität des ungestörten Lebensraums annimmt, der in der in der Lage ist die originale Amphibiengemeinschaft aus Waldspezialisten (FS) zu erhalten. Im dritten Artikel untersuche ich die Faktoren, die zu einem erhöhten Milbenbefall in den Amphibiengesellschaften des TNP führen. Ich fand heraus, dass die Wirts-Parasit-Beziehung zwischen Milben der Gattung Endotrombicula sehr spezifisch auf Frösche der Gattung Phrynobatrachus zugeschnitten ist, da offensichtlich nur die vier Arten P. phyllophilus, P. alleni, P. villiersi und P. plicatus befallen werden. Ebenso zeigte sich der Milbenbefall abhängig von der Art (höchste Prävalenz bei P. phyllophilus gefolgt von P. alleni), des Geschlechts (höhere Prävalenz bei Männchen als bei Weibchen, sowohl bei P. alleni und P. phyllophilus), des Alters (höhere Prävalenz bei Erwachsenen als bei Jungtieren in P. alleni) sowie der Jahreszeit (höhere Prävalenz während der Regenzeit im Vergleich zur Trockenzeit bei P. phyllophilus). Ich diskutiere diese Ergebnisse mit Bezug auf die Ökologie der Endotrombicula-Milben, die stark von feuchten Bedingungen abhängig sind, sowie die Überschneidung dieser Bedingungen mit denen der Wirtsfroscharten überschneiden. Des Weiteren beobachtete ich, dass die Prävalenz des Milbenbefalls in den letzten 15 Jahren (1999-2000 bis 2016-2017) abgenommen hat. Dieser steht möglicherweise im Zusammenhang mit den lokalen Auswirkungen des Klimawandels, was die in den letzten Jahren deutlich zurückgegangenen Niederschläge erklären würde. Meine Arbeiten zeigen, dass das Verständnis der Vielfalt westafrikanischer Amphibien noch lange nicht vollständig ist. Es zeigt sich, dass weiterhin Forschungsarbeit geleistet werden muss, um den tatsächlichen Amphibienreichtum besser abschätzen zu können. Darüber hinaus habe ich gezeigt, dass sich Amphibiengemeinschaften in abgeholzten Wälder zurück zum ursprünglicheren Zustand regenerieren können, was die Bedeutung unterstreicht, genutzten Wäldern ausreichend Zeit zu lassen, um sich zu regenerieren. Ob die Milbenprävalenz tatsächlich auf Grund des Klimawandels abnahm, sollte in Zukunft genauer untersucht werden. / Environmental changes due to both natural phenomena and/or human disturbance (i.e. habitat loss, disturbance and fragmentation) are important factors contributing to global species declines. Commercial logging is amongst the greatest contributor to this disturbance resulting in widespread biodiversity declines. In tropical rainforests, particularly those of West Africa, this is particularly troubling as diverse vertebrate assemblages are subject to heavy commercial logging. Previous studies have identified negative impacts of these logging practices on the taxonomic and functional diversity of amphibian communities and species. Furthermore, logging and other environmental changes may affect host-parasite interactions, resulting in exacerbated negative impacts of these pressures and reduced survivability of host species. As such, determining the effects of logging on amphibians, their subsequent recovery following selective logged forest, and the effects of environmental change on host-parasite relationships, will be paramount for informing future conservation action. In this thesis, I aim to determine how amphibian community dynamics shift over a regeneration gradient following disturbance (logging), and how this disturbance influences amphibian-parasite interactions. I use combined data sets (amphibian, parasite and habitat) from two time periods 15 years apart (1999-2000 and 2016-2017) collected in identical sites (logged forest since 45 years and old growth forest) within Taï National Park (TNP) Ivory Coast, in order to examine the adaptive capacities of frogs and their parasites to changing environments. In the first paper, I underline the importance of forest, even small, as potential source of undescribed biodiversity. In that small swamp forest, never survey before located in southeastern Ivory Coast, I found a new leaf-litter species of the Phrynobatrachus genus. Based on morphological characteristics, considerable molecular genetic distance to other West African Phrynobatrachus species, as well as advertisement calls, I describe Phrynobatrachus tanoeensis sp. nov. as a species new to science. In the second paper, I investigate the resilience of West African frogs in forests selectively logged over 45 years ago by comparing data (amphibian diversity, abundance, composition and habitat) from previously logged and old growth forest over two time periods (2000 and 2016-2017). I found that the structure of previously logged forest slowly recovered toward old growth forest states over the course of 45 years, with most visible changes occurring in the last 15 years. I also found no changes in amphibian diversity and abundance in the previously logged forest over time but observed a progressive convergence of amphibian composition in previously logged forests toward that of unlogged forest amphibian communities. In contrast, several forest specialist species (FS) recovered, whilst forest generalist (FG) species declined in the previously logged forest over the 15 years sampling period. These findings suggest that 45 years since logging activities the previously logged forest gradually provides habitat heterogeneity capable of maintaining FS amphibian species and more intact amphibian communities. In paper 3, I investigate the factors leading to increased mite infestation in the amphibian assemblages of TNP. I found that mites of the Endotrombicula genus seem to be specific to Phrynobatrachus frogs and infested only four leaf-litter species (P. phyllophilus, P. alleni, P. villiersi and P. plicatus). I also found that mite infestation was associated with species (highest prevalence in P. phyllophilus followed by P. alleni), sex (higher prevalence in males than females in P. alleni and P. phyllophilus), age (higher adult prevalence than juveniles in P alleni) as well as season (higher prevalence during the wet compared to the dry season in P. phyllophilus). I discuss these findings with reference to the ecology of Endotrombicula mites which rely heavily on humid conditions, conditions which overlap with the reproductive requirements of the host taxa. Additionally, I observed that the prevalence of mite infestation decreased over the last 15 years (1999-2000 to 2016-2017). This decreased mite infestation over time is potentially linked to local climate change, which exhibited distinctly lower rainfall in recent years. These studies show that West African amphibian diversity is far to be complete. Thus, more survey work needs to be done in order to have an idea of amphibian richness. Additionally, I showed that to environmental changes in the context of recovery following logging have a positive impact on amphibian. Forest amphibian community recovers in the previously logged forest, which highlight the importance to leave those forest to regenerate. However, although mite prevalence decreased over time, future research of post logging restoration and climate change impact on mite prevalence need be more investigate.

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<p>Course-based Undergraduate Research Experiences (CUREs) have been described in a range of educational contexts. Although various learning objectives, termed anticipated learning outcomes (ALOs) in this project, have been proposed, processes for identifying them may not be rigorous or well-documented, which can lead to inappropriate assessment and speculation about what students actually learn from CUREs. Additionally, evaluation of CUREs has primarily relied on student and instructor perception data rather than more reliable measures of learning.This dissertation investigated a novel biochemistry laboratory curriculum for a Course-based Undergraduate Research Experience (CURE) known as the Biochemistry Authentic Scientific Inquiry Lab (BASIL). Students participating in this CURE use a combination of computational and biochemical wet-lab techniques to elucidate the function of proteins of known structure but unknown function. The goal of the project was to evaluate the efficacy of the BASIL CURE curriculum for developing students’ research abilities across implementations. Towards achieving this goal, we addressed the following four research questions (RQs): <b>RQ1</b>) How can ALOs be rigorously identified for the BASIL CURE; <b>RQ2</b>) How can the identified ALOs be used to develop a matrix that characterizes the BASIL CURE; <b>RQ3</b>) What are students’ perceptions of their knowledge, confidence and competence regarding their abilities to perform the top-rated ALOs for this CURE; <b>RQ4</b>) What are appropriate assessments for student achievement of the identified ALOs and what is the nature of student learning, and related difficulties, developed by students during the BASIL CURE? To address these RQs, this project focused on the development and use of qualitative and quantitative methods guided by constructivism and situated cognition theoretical frameworks. Data was collected using a range of instruments including, content analysis, Qualtrics surveys, open-ended questions and interviews, in order to identify ALOs and to determine student learning for the BASIL CURE. Analysis of the qualitative data was through inductive coding guided by the concept-reasoning-mode (CRM) model and the assessment triangle, while analysis of quantitative data was done by using standard statistical techniques (e.g. conducting a parried t-test and effect size). The results led to the development of a novel method for identifying ALOs, namely a process for identifying course-based undergraduate research abilities (PICURA; RQ1; Irby, Pelaez, & Anderson 2018b). Application of PICURA to the BASIL CURE resulted in the identification and rating by instructors of a wide range of ALOs, termed course-based undergraduate research abilities (CURAs), which were formulated into a matrix (RQs 2; Irby, Pelaez, & Anderson, 2018a,). The matrix was, in turn, used to characterize the BASIL CURE and to inform the design of student assessments aimed at evaluating student development of the identified CURAs (RQs 4; Irby, Pelaez, & Anderson, 2018a). Preliminary findings from implementation of the open-ended assessments in a small case study of students, revealed a range of student competencies for selected top-rated CURAs as well as evidence for student difficulties (RQ4). In this way we were able to confirm that students are developing some of the ALOs as actual learning outcomes which we term VLOs or verified learning outcomes. In addition, a participant perception indicator (PPI) survey was used to gauge students’ perceptions of their gains in knowledge, experience, and confidence during the BASIL CURE and, therefore, to inform which CURAs should be specifically targeted for assessment in specific BASIL implementations (RQ3;). These results indicate that, across implementations of the CURE, students perceived significant gains with large effect sizes in their knowledge, experience, and confidence for items on the PPI survey (RQ3;). In our view, the results of this dissertation will make important contributions to the CURE literature, as well as to the biochemistry education and assessment literature in general. More specifically, it will significantly improve understanding of the nature of student learning from CUREs and how to identify ALOs and design assessments that reveal what students actually learn from such CUREs - an area where there has been a dearth of available knowledge in the past. The outcomes of this dissertation could also help instructors and administrators identify and align assessments with the actual features of a CURE (or courses in general), use the identified CURAs to ensure the material fits departmental or university needs, and evaluate the benefits of students participating in these innovative curricula. Future research will focus on expanding the development and validation of assessments so that practitioners can better evaluate the efficacy of their CUREs for developing the research competencies of their undergraduate students and continue to render improvements to their curricula.</p>