@phdthesis{Loewe2008,
  author    = {L{\"o}we, Tobias},
  title     = {Untersuchung von gene-drive-Strategien als neue Interventionsstrategien zur Eind{\"a}mmung der Malaria},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-28750},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {In der vorliegenden Arbeit haben wir unter Nutzung bioinformatischer Methoden eine innovative Strategie zur Eind{\"a}mmung der Malaria entwickelt. Die genetische Modifikationsstrategie beinhaltet sowohl Manipulationen aufseiten des gef{\"a}hrlichsten Erregers, Plasmodium falciparum, als auch des Hauptvektors, Anopheles gambiae. In den Genomen beider Spezies wurden eine Reihe neuer konkreter targets identifiziert. Auch bereits beschriebene targets und Ans{\"a}tze wurden in die Strategie einbezogen bzw. weiter ausgestaltet. Bez{\"u}glich der Vektormoskitos wird die Verbreitung eines gegen{\"u}ber Plasmodien resistenten Genotyps angestrebt. Es werden einerseits effiziente nat{\"u}rliche und k{\"u}nstliche Resistenzgene diskutiert und andererseits eine bekannte Strategie zur Fixierung nat{\"u}rlicher Resistenzallele in nat{\"u}rlichen Populationen verbessert. Auf der Seite der Plasmodien erweiterten wir einen bereits von A. Burt (2003) beschriebenen Eradikationsansatz um weitere targets. Aus ethischen und evolutionsbiologischen Erw{\"a}gungen bevorzugen wir jedoch eine alternative Strategie, welche die Etablierung von in ihrer Virulenz gemilderten Parasiten zum Ziel hat. Der attenuierte Genotyp wird unter anderem durch komplexe Pathway-Remodellierungen beschrieben (L{\"o}we, Sauerborn, Schirmer, Dandekar, A refined genome engineering strategy against parasites and vectors, Manuskript beim Journal „Genome Biology" eingereicht). Da sich Mutanten in der Natur gegen Wildtyp-Organismen kaum durchsetzen k{\"o}nnen, werden zwei drive-Systeme beschrieben, welche f{\"u}r die Implementierung der genetischen Manipulationsstrategie entwickelt wurden. Beide Konstrukte wurden zur Patentierung angemeldet (Patentanmeldung U30010 DPMA bzw. Aktenzeichen 102006029354.1). Zus{\"a}tzlich zur deutschen wurde f{\"u}r eines der beiden Konstrukte eine PCT-Anmeldung eingereicht, welche in Zukunft einen internationalen Patentschutz erm{\"o}glichen soll. Es werden Kalkulationen vorgelegt, welche die Verbreitungstendenzen der Konstrukte in nat{\"u}rlichen Populationen vorhersagen. Die Beschreibung der entwickelten Konstrukte beschr{\"a}nkt sich nicht auf das prim{\"a}re Anwendungsgebiet der Arbeit (Malaria), sondern beinhaltet auch andere Anwendungsgebiete, vor allem im Bereich der Medizin und Molekularbiologie.},
  subject      = {Malaria tropica},
  language  = {de}
}
@article{BiscottiCarducciBaruccaetal.2020,
  author    = {Biscotti, Maria Assunta and Carducci, Federica and Barucca, Marco and Gerdol, Marco and Pallavicini, Alberto and Schartl, Manfred and Canapa, Adriana and Contar Adolfi, Mateus},
  title     = {The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians},
  series = {Scientific Reports},
  volume    = {10},
  journal   = {Scientific Reports},
  doi       = {10.1038/s41598-020-62408-x},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-227326},
  year      = {2020},
  abstract  = {Amphibians evolved in the Devonian period about 400 Mya and represent a transition step in tetrapod evolution. Among amphibians, high-throughput sequencing data are very limited for Caudata, due to their largest genome sizes among terrestrial vertebrates. In this paper we present the transcriptome from the fire bellied newt Cynops orientalis. Data here presented display a high level of completeness, comparable to the fully sequenced genomes available from other amphibians. Moreover, this work focused on genes involved in gametogenesis and sexual development. Surprisingly, the gsdf gene was identified for the first time in a tetrapod species, so far known only from bony fish and basal sarcopterygians. Our analysis failed to isolate fgf24 and foxl3, supporting the possible loss of both genes in the common ancestor of Rhipidistians. In Cynops, the expression analysis of genes described to be sex-related in vertebrates singled out an expected functional role for some genes, while others displayed an unforeseen behavior, confirming the high variability of the sex-related pathway in vertebrates.},
  language  = {en}
}
@phdthesis{Dornhaus2002,
  author    = {Dornhaus, Anna},
  title     = {The role of communication in the foraging process of social bees},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-3468},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2002},
  abstract  = {In the various groups of social bees, different systems of communication about food sources occur. These communication systems are different solutions to a common problem of social insects: efficiently allocating the necessary number of workers first to the task of foraging and second to the most profitable food sources. The solution chosen by each species depends on the particular ecological circumstances as well as the evolutionary history of that species. For example, the outstanding difference between the bumble bee and the honey bee system is that honey bees can communicate the location of profitable food sources to nestmates, which bumble bees cannot. To identify possible selection pressures that could explain this difference, I have quantified the benefits of communicating location in honey bees. I show that these strongly depend on the habitat, and that communicating location might not benefit bees in temperate habitats. This could be due to the differing spatial distributions of resources in different habitats, in particular between temperate and tropical regions. These distributions may be the reason why the mostly temperate-living bumble bees have never evolved a communication system that allows them to transfer information on location of food sources, whereas most tropical social bees (all honey bees and many stingless bees) are able to recruit nestmates to specific points in their foraging range. Nevertheless, I show that in bumble bees the allocation of workers to foraging is also regulated by communication. Successful foragers distribute in the nest a pheromone which alerts other bees to the presence of food. This pheromone stems from a tergite gland, the function of which had not been identified previously. Usage of a pheromone in the nest to alert other individuals to forage has not been described in other social insects, and might constitute a new mode of communicating about food sources. The signal might be modulated depending on the quality of the food source. Bees in the nest sample the nectar that has been brought into the nest. Their decision whether to go out and forage depends not only on the pheromone signal, but also on the quality of the nectar they have sampled. In this way, foraging activity of a bumble bee colony is adjusted to foraging conditions, which means most bees are allocated to foraging only if high-quality food sources are available. In addition, foraging activity is adjusted to the amount of food already stored. In a colony with full honeypots, no new bees are allocated to foraging. These results help us understand how the allocation of workers to the task of food collection is regulated according to external and internal nest conditions in bumble bees.},
  subject      = {Hummel},
  language  = {en}
}
@article{HoehneProkopovKuhletal.2021,
  author    = {H{\"o}hne, Christin and Prokopov, Dmitry and Kuhl, Heiner and Du, Kang and Klopp, Christophe and Wuertz, Sven and Trifonov, Vladimir and St{\"o}ck, Matthias},
  title     = {The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome-scale sturgeon genome},
  series = {Reviews in Aquaculture},
  volume    = {13},
  journal   = {Reviews in Aquaculture},
  number    = {3},
  doi       = {10.1111/raq.12542},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239865},
  pages     = {1709 -- 1729},
  year      = {2021},
  abstract  = {Sturgeon immunity is relevant for basic evolutionary and applied research, including caviar- and meat-producing aquaculture, protection of wild sturgeons and their re-introduction through conservation aquaculture. Starting from a comprehensive overview of immune organs, we discuss pathways of innate and adaptive immune systems in a vertebrate phylogenetic and genomic context. The thymus as a key organ of adaptive immunity in sturgeons requires future molecular studies. Likewise, data on immune functions of sturgeon-specific pericardial and meningeal tissues are largely missing. Integrating immunological and endocrine functions, the sturgeon head kidney resembles that of teleosts. Recently identified pattern recognition receptors in sturgeon require research on downstream regulation. We review first acipenseriform data on Toll-like receptors (TLRs), type I transmembrane glycoproteins expressed in membranes and endosomes, initiating inflammation and host defence by molecular pattern-induced activation. Retinoic acid-inducible gene-I-like (RIG-like) receptors of sturgeons present RNA and key sensors of virus infections in most cell types. Sturgeons and teleosts share major components of the adaptive immune system, including B cells, immunoglobulins, major histocompatibility complex and the adaptive cellular response by T cells. The ontogeny of the sturgeon innate and onset of adaptive immune genes in different organs remain understudied. In a genomics perspective, our new data on 100 key immune genes exemplify a multitude of evolutionary trajectories after the sturgeon-specific genome duplication, where some single-copy genes contrast with many duplications, allowing tissue specialization, sub-functionalization or both. Our preliminary conclusion should be tested by future evolutionary bioinformatics, involving all >1000 immunity genes. This knowledge update about the acipenseriform immune system identifies several important research gaps and presents a basis for future applications.},
  language  = {en}
}
@phdthesis{Pinkert2008,
  author    = {Pinkert, Stefan},
  title     = {The human proteome is shaped by evolution and interactions},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-35566},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {Das menschliche Genom ist seit 2001 komplett sequenziert. Ein Großteil der Proteine wurde mittlerweile beschrieben und t{\"a}glich werden bioinformatische Vorhersagen praktisch best{\"a}tigt. Als weiteres Großprojekt wurde k{\"u}rzlich die Sequenzierung des Genoms von 1000 Menschen gestartet. Trotzdem ist immer noch wenig {\"u}ber die Evolution des gesamten menschlichen Proteoms bekannt. Proteindom{\"a}nen und ihre Kombinationen sind teilweise sehr detailliert erforscht, aber es wurden noch nicht alle Dom{\"a}nenarchitekturen des Menschen in ihrer Gesamtheit miteinander verglichen. Der verwendete große hochqualitative Datensatz von Protein-Protein-Interaktionen und Komplexen stammt aus dem Jahr 2006 und erm{\"o}glicht es erstmals das menschliche Proteom mit einer vorher nicht m{\"o}glichen Genauigkeit analysieren zu k{\"o}nnen. Hochentwickelte Cluster Algorithmen und die Verf{\"u}gbarkeit von großer Rechenkapazit{\"a}t bef{\"a}higen uns neue Information {\"u}ber Proteinnetzwerke ohne weitere Laborarbeit zu gewinnen. Die vorliegende Arbeit analysiert das menschliche Proteom auf drei verschiedenen Ebenen. Zuerst wurde der Ursprung von Proteinen basierend auf ihrer Dom{\"a}nenarchitektur analysiert, danach wurden Protein-Protein-Interaktionen untersucht und schließlich erfolgte Einteilung der Proteine nach ihren vorhandenen und fehlenden Interaktionen. Die meisten bekannten Proteine enthalten mindestens eine Dom{\"a}ne und die Proteinfunktion ergibt sich aus der Summe der Funktionen der einzelnen enthaltenen Dom{\"a}nen. Proteine, die auf der gleichen Dom{\"a}nenarchitektur basieren, das heißt die die gleichen Dom{\"a}nen in derselben Reihenfolge besitzen, sind homolog und daher aus einem gemeinsamen urspr{\"u}nglichen Protein entstanden. Die Dom{\"a}nenarchitekturen der urspr{\"u}nglichen Proteine wurden f{\"u}r 750000 Proteine aus 1313 Spezies bestimmt. Die Gruppierung von Spezies und ihrer Proteine ergibt sich aus taxonomischen Daten von NCBI-Taxonomy, welche mit zus{\"a}tzlichen Informationen basierend auf molekularen Markern erg{\"a}nzt wurden. Der resultierende Datensatz, bestehend aus 5817 Dom{\"a}nen und 32868 Dom{\"a}nenarchitekturen, war die Grundlage f{\"u}r die Bestimmung des Ursprungs der Proteine aufgrund ihrer Dom{\"a}nenarchitekturen. Es wurde festgestellt, dass nur ein kleiner Teil der neu evolvierten Dom{\"a}nenarchitekturen eines Taxons gleichzeitig auch im selben Taxon neu entstandene Proteindom{\"a}nen enth{\"a}lt. Ein weiteres Ergebnis war, dass Dom{\"a}nenarchitekturen im Verlauf der Evolution l{\"a}nger und komplexer werden, und dass so verschiedene Organismen wie der Fadenwurm, die Fruchtfliege und der Mensch die gleiche Menge an unterschiedlichen Proteinen haben, aber deutliche Unterschiede in der Anzahl ihrer Dom{\"a}nenarchitekturen aufweisen. Der zweite Teil besch{\"a}ftigt sich mit der Frage wie neu entstandene Proteine Bindungen mit dem schon bestehenden Proteinnetzwerk eingehen. In fr{\"u}heren Arbeiten wurde gezeigt, dass das Protein-Interaktions-Netzwerk ein skalenfreies Netz ist. Skalenfreie Netze, wie zum Beispiel das Internet, bestehen aus wenigen Knoten mit vielen Interaktionen, genannt Hubs, und andererseits aus vielen Knoten mit wenigen Interaktionen. Man vermutet, dass zwei Mechanismen zur Entstehung solcher Netzwerke f{\"u}hren. Erstens m{\"u}ssen neue Proteine um auch Teil des Proteinnetzwerkes zu werden mit Proteinen interagieren, die bereits Teil des Netzwerkes sind. Zweitens interagieren die neuen Proteine, gem{\"a}ß der Theorie der bevorzugten Bindung, mit h{\"o}herer Wahrscheinlichkeit mit solchen Proteinen im Netzwerk, die schon an zahlreichen weiteren Protein-Interaktionen beteiligt sind. Die Human Protein Reference Database stellt ein auf Informationen aus in-vivo Experimenten beruhendes Proteinnetzwerk f{\"u}r menschliche Proteine zur Verf{\"u}gung. Basierend auf den in Kapitel I gewonnenen Informationen wurden die Proteine mit dem Ursprungstaxon ihrer Dom{\"a}nenarchitekturen versehen. Dadurch wurde gezeigt, dass ein Protein h{\"a}ufiger mit Proteinen, die im selben Taxon entstanden sind, interagiert, als mit Proteinen, die in anderen Taxa neu aufgetreten sind. Es stellte sich heraus, dass diese Interaktionsraten f{\"u}r alle Taxa deutlich h{\"o}her waren, als durch das Zufallsmodel vorhergesagt wurden. Alle Taxa enthalten den gleichen Anteil an Proteinen mit vielen Interaktionen. Diese zwei Ergebnisse sprechen dagegen, dass die bevorzugte Bindung der alleinige Mechanismus ist, der zum heutigen Aufbau des menschlichen Proteininteraktion-Netzwerks beigetragen hat. Im dritten Teil wurden Proteine basierend auf dem Vorhandensein und der Abwesenheit von Interaktionen in Gruppen eingeteilt. Proteinnetzwerke k{\"o}nnen in kleine hoch vernetzte Teile zerlegt werden, die eine spezifische Funktion aus{\"u}ben. Diese Gruppen k{\"o}nnen mit hoher statistischer Signifikanz berechnet werden, haben meistens jedoch keine biologische Relevanz. Mit einem neuen Algorithmus, welcher zus{\"a}tzlich zu Interaktionen auch Nicht-Interaktionen ber{\"u}cksichtigt, wurde ein Datensatz bestehend aus 8,756 Proteinen und 32,331 Interaktionen neu unterteilt. Eine Einteilung in elf Gruppen zeigte hohe auf Gene Ontology basierte Werte und die Gruppen konnten signifikant einzelnen Zellteilen zugeordnet werden. Eine Gruppe besteht aus Proteinen, welche wenige Interaktionen miteinander aber viele Interaktionen zu zwei benachbarten Gruppen besitzen. Diese Gruppe enth{\"a}lt eine signifikant erh{\"o}hte Anzahl an Transportproteinen und die zwei benachbarten Gruppen haben eine erh{\"o}hte Anzahl an einerseits extrazellul{\"a}ren und andererseits im Zytoplasma und an der Membran lokalisierten Proteinen. Der Algorithmus hat damit unter Beweis gestellt das die Ergebnisse nicht bloß statistisch sondern auch biologisch relevant sind. Wenn wir auch noch weit vom Verst{\"a}ndnis des Ursprungs der Spezies entfernt sind, so hat diese Arbeit doch einen Beitrag zum besseren Verst{\"a}ndnis der Evolution auf dem Level der Proteine geleistet. Im Speziellen wurden neue Erkenntnisse {\"u}ber die Beziehung von Proteindom{\"a}nen und Dom{\"a}nenarchitekturen, sowie ihre Pr{\"a}ferenzen f{\"u}r Interaktionspartner im Interaktionsnetzwerk gewonnen.},
  subject      = {Evolution},
  language  = {en}
}
@article{BorgesLinkEngstleretal.2021,
  author    = {Borges, Alyssa R. and Link, Fabian and Engstler, Markus and Jones, Nicola G.},
  title     = {The Glycosylphosphatidylinositol Anchor: A Linchpin for Cell Surface Versatility of Trypanosomatids},
  series = {Frontiers in Cell and Developmental Biology},
  volume    = {9},
  journal   = {Frontiers in Cell and Developmental Biology},
  issn      = {2296-634X},
  doi       = {10.3389/fcell.2021.720536},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249253},
  year      = {2021},
  abstract  = {The use of glycosylphosphatidylinositol (GPI) to anchor proteins to the cell surface is widespread among eukaryotes. The GPI-anchor is covalently attached to the C-terminus of a protein and mediates the protein's attachment to the outer leaflet of the lipid bilayer. GPI-anchored proteins have a wide range of functions, including acting as receptors, transporters, and adhesion molecules. In unicellular eukaryotic parasites, abundantly expressed GPI-anchored proteins are major virulence factors, which support infection and survival within distinct host environments. While, for example, the variant surface glycoprotein (VSG) is the major component of the cell surface of the bloodstream form of African trypanosomes, procyclin is the most abundant protein of the procyclic form which is found in the invertebrate host, the tsetse fly vector. Trypanosoma cruzi, on the other hand, expresses a variety of GPI-anchored molecules on their cell surface, such as mucins, that interact with their hosts. The latter is also true for Leishmania, which use GPI anchors to display, amongst others, lipophosphoglycans on their surface. Clearly, GPI-anchoring is a common feature in trypanosomatids and the fact that it has been maintained throughout eukaryote evolution indicates its adaptive value. Here, we explore and discuss GPI anchors as universal evolutionary building blocks that support the great variety of surface molecules of trypanosomatids.},
  language  = {en}
}
@phdthesis{Mitesser2006,
  author    = {Mitesser, Oliver},
  title     = {The evolution of insect life history strategies in a social context},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-22576},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2006},
  abstract  = {This thesis extends the classical theoretical work of Macevicz and Oster (1976, expanded by Oster and Wilson, 1978) on adaptive life history strategies in social insects. It focuses on the evolution of dynamic behavioural patterns (reproduction and activity) as a consequence of optimal allocation of energy and time resources. Mathematical modelling is based on detailed empirical observations in the model species Lasioglossum malachurum (Halictidae; Hymenoptera). The main topics are field observations, optimisation models for eusocial life histories, temporal variation in life history decisions, and annual colony cycles of eusocial insects.},
  subject      = {Schmalbienen},
  language  = {en}
}
@article{SiegerHovestadt2020,
  author    = {Sieger, Charlotte Sophie and Hovestadt, Thomas},
  title     = {The degree of spatial variation relative to temporal variation influences evolution of dispersal},
  series = {Oikos},
  volume    = {129},
  journal   = {Oikos},
  number    = {11},
  doi       = {10.1111/oik.07567},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239049},
  pages     = {1611 -- 1622},
  year      = {2020},
  abstract  = {In the face of ongoing global climate and land use change, organisms have multiple possibilities to cope with the modification of their environment. The two main possibilities are to either adapt locally or disperse to a more suitable habitat. The evolution of both local adaptation and dispersal interacts and can be influenced by the spatial and temporal variation (of e.g. temperature or precipitation). In an individual based model (IBM), we explore evolution of phenotypes in landscapes with varying degree of spatial relative to global temporal variation in order to examine its influence on the evolution of dispersal, niche optimum and niche width. The relationship between temporal and spatial variation did neither influence the evolution of local adaptation in the niche optimum nor of niche widths. Dispersal probability is highly influenced by the spatio-temporal relationship: with increasing spatial variation, dispersal probability decreases. Additionally, the shape of the distribution of the trait values over patch attributes switches from hump- to U-shaped. At low spatial variance more individuals emigrate from average habitats, at high spatial variance more from extreme habitats. The comparatively high dispersal probability in extreme patches of landscapes with a high spatial variation can be explained by evolutionary succession of two kinds of adaptive response. Early in the simulations, extreme patches in landscapes with a high spatial variability act as sink habitats, where population persistence depends on highly dispersive individuals with a wide niche. With ongoing evolution, local adaptation of the remaining individuals takes over, but simultaneously a possible bet-hedging strategy promotes higher dispersal probabilities in those habitats. Here, in generations that experience extreme shifts from the temporal mean of the patch attribute, the expected fitness becomes higher for dispersing individuals than for philopatric individuals. This means that under certain circumstances, both local adaptation and high dispersal probability can be selected for for coping with the projected environmental changes in the future.},
  language  = {en}
}
@phdthesis{Ankenbrand2018,
  author    = {Ankenbrand, Markus Johannes},
  title     = {Squeezing more information out of biological data - development and application of bioinformatic tools for ecology, evolution and genomics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156344},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {New experimental methods have drastically accelerated the pace and quantity at which biological data is generated. High-throughput DNA sequencing is one of the pivotal new technologies. It offers a number of novel applications in various fields of biology, including ecology, evolution, and genomics. However, together with those opportunities many new challenges arise. Specialized algorithms and software are required to cope with the amount of data, often requiring substantial training in bioinformatic methods. Another way to make those data accessible to non-bioinformaticians is the development of programs with intuitive user interfaces. In my thesis I developed analyses and programs to tackle current problems with high-throughput data in biology. In the field of ecology this covers the establishment of the bioinformatic workflow for pollen DNA meta-barcoding. Furthermore, I developed an application that facilitates the analysis of ecological communities in the context of their traits. Information from multiple public databases have been aggregated and can now be mapped automatically to existing community tables for interactive inspection. In evolution the new data are used to reconstruct phylogenetic trees from multiple genes. I developed the tool bcgTree to automate this process for bacteria. Many plant genomes have been sequenced in current years. Sequencing reads of those projects also contain data from the chloroplasts. The tool chloroExtractor supports the targeted extraction and analysis of the chloroplast genome. To compare the structure of multiple genomes specialized software is required for calculation and visualization of the relationships. I developed AliTV to address this. In contrast to existing programs for this task it allows interactive adjustments of produced graphics. Thus, facilitating the discovery of biologically relevant information. Another application I developed helps to analyze transcriptomes even if no reference genome is present. This is achieved by aggregating the different pieces of information, like functional annotation and expression level, for each transcript in a web platform. Scientists can then search, filter, subset, and visualize the transcriptome. Together the methods and tools expedite insights into biological systems that were not possible before.},
  language  = {en}
}
@unpublished{Dandekar2007,
  author    = {Dandekar, Thomas},
  title     = {Some general system properties of a living observer and the environment he explores},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33537},
  year      = {2007},
  abstract  = {In a nice assay published in Nature in 1993 the physicist Richard God III started from a human observer and made a number of witty conclusions about our future prospects giving estimates for the existence of the Berlin Wall, the human race and all the rest of the universe. In the same spirit, we derive implications for "the meaning of life, the universe and all the rest" from few principles. Adams´ absurd answer "42" tells the lesson "garbage in / garbage out" - or suggests that the question is non calculable. We show that experience of "meaning" and to decide fundamental questions which can not be decided by formal systems imply central properties of life: Ever higher levels of internal representation of the world and an escalating tendency to become more complex. An observer, "collecting observations" and three measures for complexity are examined. A theory on living systems is derived focussing on their internal representation of information. Living systems are more complex than Kolmogorov complexity ("life is NOT simple") and overcome decision limits (G{\"o}del theorem) for formal systems as illustrated for cell cycle. Only a world with very fine tuned environments allows life. Such a world is itself rather complex and hence excessive large in its space of different states - a living observer has thus a high probability to reside in a complex and fine tuned universe.},
  subject      = {Komplex <Algebra>},
  language  = {en}
}
@phdthesis{Streinzer2013,
  author    = {Streinzer, Martin},
  title     = {Sexual dimorphism of the sensory systems in bees (Hymenoptera, Apoidea) and the evolution of sex-specific adaptations in the context of mating behavior},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-78689},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Bees have had an intimate relationship with humans for millennia, as pollinators of fruit, vegetable and other crops and suppliers of honey, wax and other products. This relationship has led to an extensive understanding of their ecology and behavior. One of the most comprehensively understood species is the Western honeybee, Apis mellifera. Our understanding of sex-specific investment in other bees, however, has remained superficial. Signals and cues employed in bee foraging and mating behavior are reasonably well understood in only a handful of species and functional adaptations are described in some species. I explored the variety of sensory adaptations in three model systems within the bees. Females share a similar ecology and similar functional morphologies are to be expected. Males, engage mainly in mating behavior. A variety of male mating strategies has been described which differ in their spatiotemporal features and in the signals and cues involved, and thus selection pressures. As a consequence, males' sensory systems are more diverse than those of females. In the first part I studied adaptations of the visual system in honeybees. I compared sex and caste-specific eye morphology among 5 species (Apis andreniformis, A. cerana, A. dorsata, A. florea, A. mellifera). I found a strong correlation between body size and eye size in both female castes. Queens have a relatively reduced visual system which is in line with the reduced role of visual perception in their life history. Workers differed in eye size and functional morphology, which corresponds to known foraging differences among species. In males, the eyes are conspicuously enlarged in all species, but a disproportionate enlargement was found in two species (A. dorsata, A. florea). I further demonstrate a correlation between male visual parameters and mating flight time, and propose that light intensities play an important role in the species-specific timing of mating flights. In the second study I investigated eye morphology differences among two phenotypes of drones in the Western honeybee. Besides normal-sized drones, smaller drones are reared in the colony, and suffer from reduced reproductive success. My results suggest that the smaller phenotype does not differ in spatial resolution of its visual system, but suffers from reduced light and contrast sensitivity which may exacerbate the reduction in reproductive success caused by other factors. In the third study I investigated the morphology of the visual system in bumblebees. I explored the association between male eye size and mating behavior and investigated the diversity of compound eye morphology among workers, queens and males in 11 species. I identified adaptations of workers that correlate with distinct foraging differences among species. Bumblebee queens must, in contrast to honeybees, fulfill similar tasks as workers in the first part of their life, and correspondingly visual parameters are similar among both female castes. Enlarged male eyes are found in several subgenera and have evolved several times independently within the genus, which I demonstrate using phylogenetic informed statistics. Males of these species engage in visually guided mating behavior. I find similarities in the functional eye morphology among large-eyed males in four subgenera, suggesting convergent evolution as adaptation to similar visual tasks. In the remaining species, males do not differ significantly from workers in their eye morphology. In the fourth study I investigated the sexual dimorphism of the visual system in a solitary bee species. Males of Eucera berlandi patrol nesting sites and compete for first access to virgin females. Males have enlarged eyes and better spatial resolution in their frontal eye region. In a behavioral study, I tested the effect of target size and speed on male mate catching success. 3-D reconstructions of the chasing flights revealed that angular target size is an important parameter in male chasing behavior. I discuss similarities to other insects that face similar problems in visual target detection. In the fifth study I examined the olfactory system of E. berlandi. Males have extremely long antennae. To investigate the anatomical grounds of this elongation I studied antennal morphology in detail in the periphery and follow the sexual dimorphism into the brain. Functional adaptations were found in males (e.g. longer antennae, a multiplication of olfactory sensilla and receptor neurons, hypertrophied macroglomeruli, a numerical reduction of glomeruli in males and sexually dimorphic investment in higher order processing regions in the brain), which were similar to those observed in honeybee drones. The similarities and differences are discussed in the context of solitary vs. eusocial lifestyle and the corresponding consequences for selection acting on males.},
  subject      = {Biene},
  language  = {en}
}
@phdthesis{Schilder1999,
  author    = {Schilder, Klaus},
  title     = {Safer without Sex?},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1977},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {1999},
  abstract  = {Highly eusocial insect societies, such as all known ants, are typically characterized by a reproductive division of labor between queens, who are inseminated and reproduce, and virgin workers, who engage in foraging, nest maintenance and brood care. In most species workers have little reproductive options left: They usually produce haploid males by arrhenotokous parthenogenesis, both in the queenright and queenless condition. In the phylogenetically primitive subfamily Ponerinae reproductive caste dimorphism is much less pronounced: Ovarian morphology is rather similar in queens and workers, which additionally retain a spermatheca. In many ponerine species workers mate and may have completely replaced the queen caste. This similarity in reproductive potential provides for the evolution of diverse reproductive systems. In addition, it increases the opportunity for reproductive conflicts among nestmates substantially. Only in a handful of ant species, including Platythyrea punctata, workers are also able to rear diploid female offspring from unfertilized eggs by thelytokous parthenogenesis. The small ponerine ant P. punctata (Smith) is the only New World member of the genus reaching as far north as the southern USA, with its center of distribution in Central America and the West Indies. P. punctata occurs in a range of forest habitats including subtropical hardwood forests as well as tropical rain forests. In addition to queens, gamergates and thelytokous workers co-occur in the same species. This remarkable complexity of reproductive strategies makes P. punctata unique within ants and provides an ideal model system for the investigation of reproductive conflicts within the female caste. Colonies are usually found in rotten branches on the forest floor but may also be present in higher strata. Colonies contained on average 60 workers, with a maximum colony size of 148 workers. Queens were present in only ten percent of the colonies collected from Florida, but completely absent both from the populations studied in Barbados and Puerto Rico. Males were generally rare. In addition, morphological intermediates between workers and queens (so-called intercastes) were found in 16 colonies collected in Florida. Their thorax morphology varied from an almost worker-like to an almost queen-like thorax structure. Queen and intercaste size, however, did not differ from those of workers. Although workers taken from colonies directly after collection from the field engaged in aggressive interactions, nestmate discrimination ceased in the laboratory suggesting that recognition cues used are derived from the environment. Only one of six queens dissected was found to be inseminated but not fertile. Instead, in most queenless colonies, a single uninseminated worker monopolized reproduction by means of thelytokous parthenogenesis. A single mated, reproductive worker (gamergate) was found dominating reproduction in the presence of an inseminated alate queen only in one of the Florida colonies. The regulation of reproduction was closely examined in ten experimental groups of virgin laboratory-reared workers, in which one worker typically dominated reproduction by thelytoky despite the presence of several individuals with elongated, developing ovaries. In each group only one worker was observed to oviposit. Conflict over reproduction was intense consisting of ritualized physical aggression between some nestmates including antennal boxing, biting, dragging, leap and immobilization behaviors. The average frequency of interactions was low. Aggressive interactions allowed to construct non-linear matrices of social rank. On average, only five workers were responsible for 90 percent of total agonistic interactions. In 80 percent of the groups the rate of agonistic interactions increased after the experimental removal of the reproductive worker. While antennal boxing and biting were the most frequent forms of agonistic behaviors both before and after the removal, biting and dragging increased significantly after the removal indicating that agonistic interactions increased in intensity. Once a worker obtains a high social status it is maintained without the need for physical aggression. The replacement of reproductives by another worker did however not closely correlate with the new reproductive's prior social status. Age, however, had a profound influence on the individual rate of agonistic interactions that workers initiated. Especially younger adults (up to two month of age) and callows were responsible for the increase in observed aggression after the supersedure of the old reproductive. These individuals have a higher chance to become reproductive since older, foraging workers may not be able to develop their ovaries. Aggressions among older workers ceased with increasing age. Workers that already started to develop their ovaries should pose the greatest threat to any reproductive individual. Indeed, dissection of all experimental group revealed that aggression was significantly more often directed towards both individuals with undeveloped and developing ovaries as compared to workers that had degenerated ovaries. In all experimental groups reproductive dominance was achieved by callows or younger workers not older than four month. Age is a better predictor of reproductive dominance than social status as inferred from physical interactions. Since no overt conflict between genetical identical individuals is expected, in P. punctata the function of agonistic interactions in all-worker colonies, given the predominance of thelytokous parthenogenesis, remains unclear. Physical aggression could alternatively function to facilitate a smooth division of non-reproductive labor thereby increasing overall colony efficiency. Asexuality is often thought to constitute an evolutionary dead end as compared with sexual reproduction because genetic recombination is limited or nonexistent in parthenogenetic populations. Microsatellite markers were developed to investigate the consequences of thelytokous reproduction on the genetic structure of four natural populations of P. punctata. In the analysis of 314 workers taken from 51 colonies, low intraspecific levels of variation at all loci, expressed both as the number of alleles detected and heterozygosities observed, was detected. Surprisingly, there was almost no differentiation within populations. Populations rather had a clonal structure, with all individuals from all colonies usually sharing the same genotype. This low level of genotypic diversity reflects the predominance of thelytoky under natural conditions in four populations of P. punctata. In addition, the specificity of ten dinucleotide microsatellite loci developed for P. punctata was investigated in 29 ant species comprising four different subfamilies by cross-species amplification. Positive amplification was only obtained in a limited number of species indicating that sequences flanking the hypervariable region are often not sufficiently conserved to allow amplification, even within the same genus. The karyotype of P. punctata (2n = 84) is one of the highest chromosome numbers reported in ants so far. A first investigation did not show any indication of polyploidy, a phenomenon which has been reported to be associated with the occurrence of parthenogenesis. Thelytokous parthenogenesis does not appear to be a very common phenomenon in the Hymenoptera. It is patchily distributed and restricted to taxa at the distant tips of phylogenies. Within the Formicidae, thelytoky has been demonstrated only in four phylogenetically very distant species, including P. punctata. Despite its advantages, severe costs and constraints may have restricted its rapid evolution and persistence over time. The mechanisms of thelytokous parthenogenesis and its ecological correlates are reviewed for the known cases in the Hymenoptera. Investigating the occurrence of sexual reproduction in asexual lineages indicates that thelytokous parthenogenesis may not be irreversible. In P. punctata the occasional production of sexuals in some of the colonies may provide opportunity for outbreeding and genetic recombination. Thelytoky can thus function as a conditional reproductive strategy. Thelytoky in P. punctata possibly evolved as an adaptation to the risk of colony orphanage or the foundation of new colonies by fission. The current adaptive value of physical aggression and the production of sexuals in clonal populations, where relatedness asymmetries are virtually absent, however is less clear. Quite contrary, thelytoky could thereby serve as the stepping stone for the subsequent loss of the queen caste in P. punctata. Although P. punctata clearly fulfills all three conditions of eusociality, the evolution of thelytoky is interpreted as a first step in a secondary reverse social evolution towards a social system more primitive than eusociality.},
  subject      = {Ameisenstaat},
  language  = {en}
}
@article{GuptaMinochaThapaetal.2022,
  author    = {Gupta, Shishir K. and Minocha, Rashmi and Thapa, Prithivi Jung and Srivastava, Mugdha and Dandekar, Thomas},
  title     = {Role of the pangolin in origin of SARS-CoV-2: an evolutionary perspective},
  series = {International Journal of Molecular Sciences},
  volume    = {23},
  journal   = {International Journal of Molecular Sciences},
  number    = {16},
  issn      = {1422-0067},
  doi       = {10.3390/ijms23169115},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-285995},
  year      = {2022},
  abstract  = {After the recent emergence of SARS-CoV-2 infection, unanswered questions remain related to its evolutionary history, path of transmission or divergence and role of recombination. There is emerging evidence on amino acid substitutions occurring in key residues of the receptor-binding domain of the spike glycoprotein in coronavirus isolates from bat and pangolins. In this article, we summarize our current knowledge on the origin of SARS-CoV-2. We also analyze the host ACE2-interacting residues of the receptor-binding domain of spike glycoprotein in SARS-CoV-2 isolates from bats, and compare it to pangolin SARS-CoV-2 isolates collected from Guangdong province (GD Pangolin-CoV) and Guangxi autonomous regions (GX Pangolin-CoV) of South China. Based on our comparative analysis, we support the view that the Guangdong Pangolins are the intermediate hosts that adapted the SARS-CoV-2 and represented a significant evolutionary link in the path of transmission of SARS-CoV-2 virus. We also discuss the role of intermediate hosts in the origin of Omicron.},
  language  = {en}
}
@phdthesis{Kubisch2012,
  author    = {Kubisch, Alexander},
  title     = {Range border formation in the light of dispersal evolution},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70639},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2012},
  abstract  = {Understanding the emergence of species' ranges is one of the most fundamental challenges in ecology. Early on, geographical barriers were identified as obvious natural constraints to the spread of species. However, many range borders occur along gradually changing landscapes, where no sharp barriers are obvious. Mechanistic explanations for this seeming contradiction incorporate environmental gradients that either affect the spatio-temporal variability of conditions or the increasing fragmentation of habitat. Additionally, biological mechanisms like Allee effects (i.e. decreased growth rates at low population sizes or densities), condition-dependent dispersal, and biological interactions with other species have been shown to severely affect the location of range margins. The role of dispersal has been in the focus of many studies dealing with range border formation. Dispersal is known to be highly plastic and evolvable, even over short ecological time-scales. However, only few studies concentrated on the impact of evolving dispersal on range dynamics. This thesis aims at filling this gap. I study the influence of evolving dispersal rates on the persistence of spatially structured populations in environmental gradients and its consequences for the establishment of range borders. More specially I investigate scenarios of range formation in equilibrium, periods of range expansion, and range shifts under global climate change ...},
  subject      = {Areal},
  language  = {en}
}
@article{BaalbergenHelwerdaSchelfhorstetal.2014,
  author    = {Baalbergen, Els and Helwerda, Renate and Schelfhorst, Rense and Castillo Cajas, Ruth F. and van Moorsel, Coline H. M. and Kundrata, Robin and Welter-Schultes, Francisco W. and Giokas, Sinos and Schilthuizen, Menno},
  title     = {Predator-Prey Interactions between Shell-Boring Beetle Larvae and Rock-Dwelling Land Snails},
  series = {PLOS ONE},
  volume    = {9},
  journal   = {PLOS ONE},
  number    = {6},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0100366},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115963},
  pages     = {e100366},
  year      = {2014},
  abstract  = {Drilus beetle larvae (Coleoptera: Elateridae) are specialized predators of land snails. Here, we describe various aspects of the predator-prey interactions between multiple Drilus species attacking multiple Albinaria (Gastropoda: Clausiliidae) species in Greece. We observe that Drilus species may be facultative or obligate Albinaria-specialists. We map geographically varying predation rates in Crete, where on average 24\% of empty shells carry fatal Drilus bore holes. We also provide first-hand observations and video-footage of prey entry and exit strategies of the Drilus larvae, and evaluate the potential mutual evolutionary impacts. We find limited evidence for an effect of shell features and snail behavioral traits on inter-and intraspecifically differing predation rates. We also find that Drilus predators adjust their predation behavior based on specific shell traits of the prey. In conclusion, we suggest that, with these baseline data, this interesting predator-prey system will be available for further, detailed more evolutionary ecology studies.},
  language  = {en}
}
@article{GarciaMatosShenetal.2014,
  author    = {Garcia, Tzintzuni I. and Matos, Isa and Shen, Yingjia and Pabuwal, Vagmita and Coelho, Maria Manuela and Wakamatsu, Yuko and Schartl, Manfred and Walter, Ronald B.},
  title     = {Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion},
  series = {PLOS ONE},
  volume    = {9},
  journal   = {PLOS ONE},
  number    = {6},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0100250},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-116000},
  pages     = {e100250},
  year      = {2014},
  abstract  = {Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82\%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18\%) displayed a wide range of ASE levels. Interestingly the majority of genes (78\%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.},
  language  = {en}
}
@article{PoethkeHovestadtMitesser2003,
  author    = {Poethke, Hans-Joachim and Hovestadt, Thomas and Mitesser, Oliver},
  title     = {Local extinction and the evolution of dispersal rates: Causes and correlations},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47718},
  year      = {2003},
  abstract  = {We present the results of individual-based simulation experiments on the evolution of dispersal rates of organisms living in metapopulations. We find conflicting results regarding the relationship between local extinction rate and evolutionarily stable (ES) dispersal rate depending on which principal mechanism causes extinction: if extinction is caused by environmental catastrophes eradicating local populations, we observe a positive correlation between extinction and ES dispersal rate; if extinction is a consequence of stochastic local dynamics and environmental fluctuations, the correlation becomes ambiguous; and in cases where extinction is caused by dispersal mortality, a negative correlation between local extinction rate and ES dispersal rate emerges. We conclude that extinction rate, which both affects and is affected by dispersal rates, is not an ideal predictor for optimal dispersal rates.},
  subject      = {Ausbreitung},
  language  = {en}
}
@article{FlorenvonRintelenHerbertetal.2020,
  author    = {Floren, Andreas and von Rintelen, Thomas and Herbert, Paul D. N. and de Araujo, Bruno Cancian and Schmidt, Stefan and Balke, Michael and Narakusumo, Raden Pramesa and Peggie, Djunijanti and Ubaidillah, Rosichon and von Rintelen, Kristina and M{\"u}ller, Tobias},
  title     = {Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests},
  series = {Scientific Reports},
  volume    = {10},
  journal   = {Scientific Reports},
  doi       = {10.1038/s41598-020-73519-w},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230565},
  year      = {2020},
  abstract  = {Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.},
  language  = {en}
}
@article{WeberOsbornFrankeetal.1977,
  author    = {Weber, Klaus and Osborn, Mary and Franke, Werner W. and Seib, Erinita and Scheer, Ulrich and Herth, Werner},
  title     = {Identification of microtubular structures in diverse plant and animal cells by immunological cross-reaction revealed in immunofluorescence microscopy using antibodies against tubulin from porcine brain},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-41383},
  year      = {1977},
  abstract  = {Antibody against tubulin from porcine brain was used to evaluate the immunological cross reactivity of tubulin from a variety of animal and plant cells. Indirect immunofluorescence microscopy revealed microtubule-containing structures including cytoplasmic microtubules, spindle microtubules, cilia and fIagella. Thus tubulin from diverse species of both mammals and plants show immunological cross-reactivity with tubulin from porcine brain. Results obtained by immunofluorescence microscopy are whenever possible compared with previously known ultrastructural results obtained by electron microscopy.},
  subject      = {Cytologie},
  language  = {en}
}
@article{GuptaOsmanogluMinochaetal.2022,
  author    = {Gupta, Shishir K. and Osmanoglu, {\"O}zge and Minocha, Rashmi and Bandi, Sourish Reddy and Bencurova, Elena and Srivastava, Mugdha and Dandekar, Thomas},
  title     = {Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information},
  series = {Frontiers in Medicine},
  volume    = {9},
  journal   = {Frontiers in Medicine},
  issn      = {2296-858X},
  doi       = {10.3389/fmed.2022.1008527},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-293953},
  year      = {2022},
  abstract  = {Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.},
  language  = {en}
}