@article{DegenHovestadtMitesseretal.2015, author = {Degen, Tobias and Hovestadt, Thomas and Mitesser, Oliver and H{\"o}lker, Franz}, title = {High female survival promotes evolution of protogyny and xexual conflict}, series = {PLoS ONE}, volume = {10}, journal = {PLoS ONE}, number = {3}, doi = {10.1371/journal.pone.0118354}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143586}, pages = {e0118354}, year = {2015}, abstract = {Existing models explaining the evolution of sexual dimorphism in the timing of emergence (SDT) in Lepidoptera assume equal mortality rates for males and females. The limiting assumption of equal mortality rates has the consequence that these models are only able to explain the evolution of emergence of males before females, i.e. protandry-the more common temporal sequence of emergence in Lepidoptera. The models fail, however, in providing adaptive explanations for the evolution of protogyny, where females emerge before males, but protogyny is not rare in insects. The assumption of equal mortality rates seems too restrictive for many insects, such as butterflies. To investigate the influence of unequal mortality rates on the evolution of SDT, we present a generalised version of a previously published model where we relax this assumption. We find that longer life-expectancy of females compared to males can indeed favour the evolution of protogyny as a fitness enhancing strategy. Moreover, the encounter rate between females and males and the sex-ratio are two important factors that also influence the evolution of optimal SDT. If considered independently for females and males the predicted strategies can be shown to be evolutionarily stable (ESS). Under the assumption of equal mortality rates the difference between the females' and males' ESS remains typically very small. However, female and male ESS may be quite dissimilar if mortality rates are different. This creates the potential for an 'evolutionary conflict' between females and males. Bagworm moths (Lepidoptera: Psychidae) provide an exemplary case where life-history attributes are such that protogyny should indeed be the optimal emergence strategy from the males' and females' perspectives: (i) Female longevity is considerably larger than that of males, (ii) encounter rates between females and males are presumably low, and (iii) females mate only once. Protogyny is indeed the general mating strategy found in the bagworm family.}, language = {en} } @article{DeelemanReinholdMillerFloren2016, author = {Deeleman-Reinhold, Christa L. and Miller, Jeremy and Floren, Andreas}, title = {Depreissia decipiens, an enigmatic canopy spider from Borneo revisited (Araneae, Salticidae), with remarks on the distribution and diversity of canopy spiders in Sabah, Borneo}, series = {ZooKeys}, volume = {556}, journal = {ZooKeys}, doi = {10.3897/zookeys.556.6174}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168342}, pages = {1-17}, year = {2016}, abstract = {Depreissia is a little known genus comprising two hymenopteran-mimicking species, one found in Central Africa and one in the north of Borneo. The male of D. decipiens is redescribed, the female is described for the first time. The carapace is elongated, dorsally flattened and rhombus-shaped, the rear of the thorax laterally depressed and transformed, with a pair of deep pits; the pedicel is almost as long as the abdomen. The male palp is unusual, characterized by the transverse deeply split membranous tegulum separating a ventral part which bears a sclerotized tegular apophysis and a large dagger-like retrodirected median apophysis. The female epigyne consists of one pair of large adjacent spermathecae and very long copulatory ducts arising posteriorly and rising laterally alongside the spermathecae continuing in several vertical and horizontal coils over the anterior surface. Relationships within the Salticidae are discussed and an affinity with the Cocalodinae is suggested. Arguments are provided for a hypothesis that D. decipiens is not ant-mimicking as was previously believed, but is a mimic of polistinine wasps. The species was found in the canopy in the Kinabalu area only, in primary and old secondary rainforest at 200-700 m.a.s.l. Overlap of canopy-dwelling spider species with those in the understorey are discussed and examples of species richness and endemism in the canopy are highlighted. Canopy fogging is a very efficient method of collecting for most arthropods. The canopy fauna adds an extra dimension to the known biodiversity of the tropical rainforest. In southeast Asia, canopy research has been neglected, inhibiting evaluation of comparative results of this canopy project with that from other regions. More use of fogging as a collecting method would greatly improve insight into the actual species richness and species distribution in general.}, language = {en} } @article{DeekenGohlkeScholzetal.2013, author = {Deeken, Rosalia and Gohlke, Jochen and Scholz, Claus-Juergen and Kneitz, Susanne and Weber, Dana and Fuchs, Joerg and Hedrich, Rainer}, title = {DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors}, series = {PLoS Genetics}, journal = {PLoS Genetics}, doi = {10.1371/journal.pgen.1003267}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96318}, year = {2013}, abstract = {Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA-encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown gall development is known to be accompanied by global changes in transcription, metabolite levels, and physiological processes. High levels of abscisic acid (ABA) in crown galls regulate expression of drought stress responsive genes and mediate drought stress acclimation, which is essential for wild-type-like tumor growth. An impact of epigenetic processes such as DNA methylation on crown gall development has been suggested; however, it has not yet been investigated comprehensively. In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. Bisulfite sequencing analysis revealed that the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. Nevertheless, the oncogenes were susceptible to siRNA-mediated methylation, which inhibited their expression and subsequently crown gall growth. Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. Mutants with reduced non-CG methylation developed larger tumors than the wild-type controls, indicating that hypermethylation inhibits plant tumor growth. The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. Genes known to be transcriptionally inhibited by ABA and methylated in crown galls became promoter methylated upon treatment of A. thaliana with ABA. This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. In summary, our studies provide evidence that epigenetic processes regulate gene expression, physiological processes, and the development of crown gall tumors.}, language = {en} } @article{DedukhDaCruzKneitzetal.2022, author = {Dedukh, Dmitrij and Da Cruz, Irene and Kneitz, Susanne and Marta, Anatolie and Ormanns, Jenny and Tichop{\´a}d, Tom{\´a}š and Lu, Yuan and Alsheimer, Manfred and Janko, Karel and Schartl, Manfred}, title = {Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa}, series = {Chromosome Research}, volume = {30}, journal = {Chromosome Research}, number = {4}, doi = {10.1007/s10577-022-09708-2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325128}, pages = {443-457}, year = {2022}, abstract = {Unisexual reproduction, which generates clonal offspring, is an alternative strategy to sexual breeding and occurs even in vertebrates. A wide range of non-sexual reproductive modes have been described, and one of the least understood questions is how such pathways emerged and how they mechanistically proceed. The Amazon molly, Poecilia formosa, needs sperm from males of related species to trigger the parthenogenetic development of diploid eggs. However, the mechanism, of how the unreduced female gametes are produced, remains unclear. Cytological analyses revealed that the chromosomes of primary oocytes initiate pachytene but do not proceed to bivalent formation and meiotic crossovers. Comparing ovary transcriptomes of P. formosa and its sexual parental species revealed expression levels of meiosis-specific genes deviating from P. mexicana but not from P. latipinna. Furthermore, several meiosis genes show biased expression towards one of the two alleles from the parental genomes. We infer from our data that in the Amazon molly diploid oocytes are generated by apomixis due to a failure in the synapsis of homologous chromosomes. The fact that this failure is not reflected in the differential expression of known meiosis genes suggests the underlying molecular mechanism may be dysregulation on the protein level or misexpression of a so far unknown meiosis gene, and/or hybrid dysgenesis because of compromised interaction of proteins from diverged genomes.}, language = {en} } @article{DechaudVolffSchartletal.2019, author = {Dechaud, Corentin and Volff, Jean-Nicolas and Schartl, Manfred and Naville, Magali}, title = {Sex and the TEs: transposable elements in sexual development and function in animals}, series = {Mobile DNA}, volume = {10}, journal = {Mobile DNA}, doi = {10.1186/s13100-019-0185-0}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-202510}, pages = {42}, year = {2019}, abstract = {Transposable elements are endogenous DNA sequences able to integrate into and multiply within genomes. They constitute a major source of genetic innovations, as they can not only rearrange genomes but also spread ready-to-use regulatory sequences able to modify host gene expression, and even can give birth to new host genes. As their evolutionary success depends on their vertical transmission, transposable elements are intrinsically linked to reproduction. In organisms with sexual reproduction, this implies that transposable elements have to manifest their transpositional activity in germ cells or their progenitors. The control of sexual development and function can be very versatile, and several studies have demonstrated the implication of transposable elements in the evolution of sex. In this review, we report the functional and evolutionary relationships between transposable elements and sexual reproduction in animals. In particular, we highlight how transposable elements can influence expression of sexual development genes, and how, reciprocally, they are tightly controlled in gonads. We also review how transposable elements contribute to the organization, expression and evolution of sexual development genes and sex chromosomes. This underscores the intricate co-evolution between host functions and transposable elements, which regularly shift from a parasitic to a domesticated status useful to the host.}, language = {en} } @article{dePazAsisHolzschuhetal.2023, author = {de Paz, V{\´i}ctor and As{\´i}s, Josep D. and Holzschuh, Andrea and Ba{\~n}os-Pic{\´o}n, Laura}, title = {Effects of traditional orchard abandonment and landscape context on the beneficial arthropod community in a Mediterranean agroecosystem}, series = {Insects}, volume = {14}, journal = {Insects}, number = {3}, issn = {2075-4450}, doi = {10.3390/insects14030277}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311190}, year = {2023}, abstract = {Agricultural abandonment is one of the main land-use changes in Europe, and its consequences on biodiversity are context- and taxa-dependent. While several studies have worked on this topic, few have focused on traditional orchards, especially in different landscapes and under a Mediterranean climate. In this context, we aimed to determine the effects of almond orchard abandonment on the communities of three groups of beneficial arthropods and the role of the landscape context in modulating these effects. Between February and September 2019, four samplings were carried out in twelve almond orchards (three abandoned and three traditional (active orchards under traditional agricultural management) located in simple landscapes as well as three abandoned and three traditional in complex landscapes). Abandoned and traditional almond orchards harbor different arthropod communities and diversity metrics that are strongly conditioned by seasonality. Abandoned orchards can favor pollinators and natural enemies, providing alternative resources in simple landscapes. However, the role that abandoned orchards play in simple landscapes disappears as the percentage of semi-natural habitats in the landscape increases. Our results show that landscape simplification, through the loss of semi-natural habitats, has negative consequences on arthropod biodiversity, even in traditional farming landscapes with small fields and high crop diversity.}, language = {en} } @article{DePalmaAbrahamczykAizenetal.2016, author = {De Palma, Adriana and Abrahamczyk, Stefan and Aizen, Marcelo A. and Albrecht, Matthias and Basset, Yves and Bates, Adam and Blake, Robin J. and Boutin, C{\´e}line and Bugter, Rob and Connop, Stuart and Cruz-L{\´o}pez, Leopoldo and Cunningham, Saul A. and Darvill, Ben and Diek{\"o}tter, Tim and Dorn, Silvia and Downing, Nicola and Entling, Martin H. and Farwig, Nina and Felicioli, Antonio and Fonte, Steven J. and Fowler, Robert and Franzen, Markus Franz{\´e}n and Goulson, Dave and Grass, Ingo and Hanley, Mick E. and Hendrix, Stephen D. and Herrmann, Farina and Herzog, Felix and Holzschuh, Andrea and Jauker, Birgit and Kessler, Michael and Knight, M. E. and Kruess, Andreas and Lavelle, Patrick and Le F{\´e}on, Violette and Lentini, Pia and Malone, Louise A. and Marshall, Jon and Mart{\´i}nez Pach{\´o}n, Eliana and McFrederick, Quinn S. and Morales, Carolina L. and Mudri-Stojnic, Sonja and Nates-Parra, Guiomar and Nilsson, Sven G. and {\"O}ckinger, Erik and Osgathorpe, Lynne and Parra-H, Alejandro and Peres, Carlos A. and Persson, Anna S. and Petanidou, Theodora and Poveda, Katja and Power, Eileen F. and Quaranta, Marino and Quintero, Carolina and Rader, Romina and Richards, Miriam H. and Roulston, T'ai and Rousseau, Laurent and Sadler, Jonathan P. and Samneg{\aa}rd, Ulrika and Schellhorn, Nancy A. and Sch{\"u}epp, Christof and Schweiger, Oliver and Smith-Pardo, Allan H. and Steffan-Dewenter, Ingolf and Stout, Jane C. and Tonietto, Rebecca K. and Tscharntke, Teja and Tylianakis, Jason M. and Verboven, Hans A. F. and Vergara, Carlos H. and Verhulst, Jort and Westphal, Catrin and Yoon, Hyung Joo and Purvis, Andy}, title = {Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, doi = {10.1038/srep31153}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167642}, pages = {31153}, year = {2016}, abstract = {Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.}, language = {en} } @article{DeLiraRamanSchulzeetal.2020, author = {De Lira, Maria Nathalia and Raman, Sudha Janaki and Schulze, Almut and Schneider-Schaulies, Sibylle and Avota, Elita}, title = {Neutral Sphingomyelinase-2 (NSM 2) Controls T Cell Metabolic Homeostasis and Reprogramming During Activation}, series = {Frontiers in Molecular Biosciences}, volume = {7}, journal = {Frontiers in Molecular Biosciences}, issn = {2296-889X}, doi = {10.3389/fmolb.2020.00217}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-211311}, year = {2020}, abstract = {Neutral sphingomyelinase-2 (NSM2) is a member of a superfamily of enzymes responsible for conversion of sphingomyelin into phosphocholine and ceramide at the cytosolic leaflet of the plasma membrane. Upon specific ablation of NSM2, T cells proved to be hyper-responsive to CD3/CD28 co-stimulation, indicating that the enzyme acts to dampen early overshooting activation of these cells. It remained unclear whether hyper-reactivity of NSM2-deficient T cells is supported by a deregulated metabolic activity in these cells. Here, we demonstrate that ablation of NSM2 activity affects metabolism of the quiescent CD4\(^+\) T cells which accumulate ATP in mitochondria and increase basal glycolytic activity. This supports enhanced production of total ATP and metabolic switch early after TCR/CD28 stimulation. Most interestingly, increased metabolic activity in resting NSM2-deficient T cells does not support sustained response upon stimulation. While elevated under steady-state conditions in NSM2-deficient CD4\(^+\) T cells, the mTORC1 pathway regulating mitochondria size, oxidative phosphorylation, and ATP production is impaired after 24 h of stimulation. Taken together, the absence of NSM2 promotes a hyperactive metabolic state in unstimulated CD4\(^+\) T cells yet fails to support sustained T cell responses upon antigenic stimulation.}, language = {en} } @phdthesis{Das2018, author = {Das, Sudip}, title = {Genome-wide identification of virulence-associated genes in Staphylococcus aureus using Transposon insertion-site deep sequencing}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143362}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Staphylococcus aureus asymptomatically colonises one third of the healthy human population, finding its niche in the nose and on skin. Apart from being a commensal, it is also an important opportunistic human pathogen capable of destructing tissue, invading host cells and killing them from within. This eventually contributes to severe hospital- and community-acquired infections. Methicillin-resistant Staphylococcus aureus (MRSA), resistant to commonly used antibiotics are protected when residing within the host cell. This doctoral thesis is focused on the investigation of staphylococcal factors governing intracellular virulence and subsequent host cell death. To initiate an unbiased approach to conduct this study, complex S. aureus mutant pools were generated using transposon insertional mutagenesis. Genome-wide infection screens were performed using these S. aureus transposon mutant pools in vitro and in vivo, followed by analysis using Transposon insertion site deep sequencing (Tn-seq) technology. Amongst several other factors, this study identified a novel regulatory system in S. aureus that controls pathogen-induced host cytotoxicity and intra-host survival. The primary components of this system are an AraC-family transcription regulator called Repressor of surface proteins (Rsp) and a virulence associated non-coding RNA, SSR42. Mutants within rsp exhibit enhanced intra-host survival in human epithelial cells and delayed host cytotoxicity. Global gene-expression profiling by RNA-seq demonstrated that Rsp controls the expression of SSR42, several cytotoxins and other bacterial factors directed against the host immune system. Rsp enhances S. aureus toxin response when triggered by hydrogen peroxide, an antimicrobial substance employed by neutrophils to destroy pathogens. Absence of rsp reduces S. aureus-induced neutrophil damage and early lethality during mouse pneumonia, but still permits blood stream infection. Intriguingly, S. aureus lacking rsp exhibited enhanced survival in human macrophages, which hints towards a Trojan horse-like phenomenon and could facilitate dissemination within the host. Hence, Rsp emerged as a global regulator of bacterial virulence, which has an impact on disease progression with prolonged intra-cellular survival, delayed-lethality but allows disseminated manifestation of disease. Moreover, this study exemplifies the use of genome-wide approaches as useful resources for identifying bacterial factors and deduction of its pathogenesis.}, subject = {Staphylococcus aureus}, language = {en} } @article{DapergolaMenegazziRaabeetal.2021, author = {Dapergola, Eleni and Menegazzi, Pamela and Raabe, Thomas and Hovhanyan, Anna}, title = {Light Stimuli and Circadian Clock Affect Neural Development in Drosophila melanogaster}, series = {Frontiers in Cell and Developmental Biology}, volume = {9}, journal = {Frontiers in Cell and Developmental Biology}, issn = {2296-634X}, doi = {10.3389/fcell.2021.595754}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-231049}, year = {2021}, abstract = {Endogenous clocks enable organisms to adapt cellular processes, physiology, and behavior to daily variation in environmental conditions. Metabolic processes in cyanobacteria to humans are under the influence of the circadian clock, and dysregulation of the circadian clock causes metabolic disorders. In mouse and Drosophila, the circadian clock influences translation of factors involved in ribosome biogenesis and synchronizes protein synthesis. Notably, nutrition signals are mediated by the insulin receptor/target of rapamycin (InR/TOR) pathways to regulate cellular metabolism and growth. However, the role of the circadian clock in Drosophila brain development and the potential impact of clock impairment on neural circuit formation and function is less understood. Here we demonstrate that changes in light stimuli or disruption of the molecular circadian clock cause a defect in neural stem cell growth and proliferation. Moreover, we show that disturbed cell growth and proliferation are accompanied by reduced nucleolar size indicative of impaired ribosomal biogenesis. Further, we define that light and clock independently affect the InR/TOR growth regulatory pathway due to the effect on regulators of protein biosynthesis. Altogether, these data suggest that alterations in InR/TOR signaling induced by changes in light conditions or disruption of the molecular clock have an impact on growth and proliferation properties of neural stem cells in the developing Drosophila brain.}, language = {en} } @article{DannhaeuserMrestaniGundelachetal.2022, author = {Dannh{\"a}user, Sven and Mrestani, Achmed and Gundelach, Florian and Pauli, Martin and Komma, Fabian and Kollmannsberger, Philip and Sauer, Markus and Heckmann, Manfred and Paul, Mila M.}, title = {Endogenous tagging of Unc-13 reveals nanoscale reorganization at active zones during presynaptic homeostatic potentiation}, series = {Frontiers in Cellular Neuroscience}, volume = {16}, journal = {Frontiers in Cellular Neuroscience}, issn = {1662-5102}, doi = {10.3389/fncel.2022.1074304}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-299440}, year = {2022}, abstract = {Introduction Neurotransmitter release at presynaptic active zones (AZs) requires concerted protein interactions within a dense 3D nano-hemisphere. Among the complex protein meshwork the (M)unc-13 family member Unc-13 of Drosophila melanogaster is essential for docking of synaptic vesicles and transmitter release. Methods We employ minos-mediated integration cassette (MiMIC)-based gene editing using GFSTF (EGFP-FlAsH-StrepII-TEV-3xFlag) to endogenously tag all annotated Drosophila Unc-13 isoforms enabling visualization of endogenous Unc-13 expression within the central and peripheral nervous system. Results and discussion Electrophysiological characterization using two-electrode voltage clamp (TEVC) reveals that evoked and spontaneous synaptic transmission remain unaffected in unc-13\(^{GFSTF}\) 3rd instar larvae and acute presynaptic homeostatic potentiation (PHP) can be induced at control levels. Furthermore, multi-color structured-illumination shows precise co-localization of Unc-13\(^{GFSTF}\), Bruchpilot, and GluRIIA-receptor subunits within the synaptic mesoscale. Localization microscopy in combination with HDBSCAN algorithms detect Unc-13\(^{GFSTF}\) subclusters that move toward the AZ center during PHP with unaltered Unc-13\(^{GFSTF}\) protein levels.}, language = {en} } @article{DannerKellerHaerteletal.2017, author = {Danner, Nadja and Keller, Alexander and H{\"a}rtel, Stephan and Steffan-Dewenter, Ingolf}, title = {Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen}, series = {PLoS ONE}, volume = {12}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal.pone.0183716}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170424}, pages = {e0183716}, year = {2017}, abstract = {The availability of pollen in agricultural landscapes is essential for the successful growth and reproduction of honey bee colonies (Apis mellifera L.). The quantity and diversity of collected pollen can influence the growth and health of honey bee colonies, but little is known about the influence of landscape structure on pollen diet. In a field experiment, we rotated 16 honey bee colonies across 16 agricultural landscapes, used traps to collect samples of collected pollen and observed intra-colonial dance communication to gain information about foraging distances. DNA metabarcoding was applied to analyze mixed pollen samples. Neither the amount of collected pollen nor pollen diversity was related to landscape diversity. However, we found a strong seasonal variation in the amount and diversity of collected pollen in all sites independent of landscape diversity. The observed increase in foraging distances with decreasing landscape diversity suggests that honey bees compensated for lower landscape diversity by increasing their pollen foraging range in order to maintain pollen amount and diversity. Our results underscore the importance of a diverse pollen diet for honey bee colonies. Agri-environmental schemes aiming to support pollinators should focus on possible spatial and temporal gaps in pollen availability and diversity in agricultural landscapes.}, language = {en} } @phdthesis{Danner2017, author = {Danner, Nadja}, title = {Honey bee foraging in agricultural landscapes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139322}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {1. Today honey bee colonies face a wide range of challenges in modern agricultural landscapes which entails the need for a comprehensive investigation of honey bees in a landscape context and the assessment of environmental risks. Within this dissertation the pollen foraging of honey bee colonies is studied in different agricultural landscapes to gain insight into the use of pollen resources and the influence of landscape structure across the season. General suggestions for landscape management to support honey bees and other pollinators are derived. 2. Decoding of waggle dances and a subsequent spatial foraging analysis are used as methods in Chapters 4 and 5 to study honey bee colonies in agricultural landscapes. The recently developed metabarcoding of mixed pollen samples was applied for the first time in honey bee foraging ecology and allowed for a detailed analysis of pollen, that was trapped from honey bees in front hive entrances (Chapter 6). 3. Pollen identification through molecular sequencing and DNA barcoding has been proposed as an alternative approach to light microscopy, which still is a tedious and error-prone task. In this study we assessed mixed pollen probes through next-generation sequencing and developed a bioinformatic workflow to analyse these high-throughput data with a newly created reference database. To evaluate the feasibility, we compared results from classical identification based on light microscopy from the same samples with our sequencing results. Abundance estimations from sequencing data were significantly correlated with counted abundances through light microscopy. Next-generation sequencing thus presents a useful and efficient workflow to identify pollen at the genus and species level without requiring specialized palynological expert knowledge. 4. During maize flowering, four observation hives were placed in and rotated between 11 landscapes covering a gradient in maize acreage. A higher foraging frequency on maize fields compared to other landuse types showed that maize is an intensively used pollen resource for honey bee colonies. Mean foraging distances were significantly shorter for maize pollen than for other pollen origins, indicating that effort is put into collecting a diverse pollen diet. The percentage of maize pollen foragers did not increase with maize acreage in the landscape and was not reduced by grassland area as an alternative pollen resource. Our findings allow estimating the distance-related exposure risk of honey bee colonies to pollen from surrounding maize fields treated with systemic insecticides. 5. It is unknown how an increasing area of mass-flowering crops like oilseed rape (OSR) or a decrease of semi-natural habitats (SNH) change the temporal and spatial availability of pollen resources for honey bee colonies, and thus foraging distances and frequency in different habitat types. Sixteen observation hives were placed in and rotated between 16 agricultural landscapes with independent gradients of OSR and SNH area within 2 km to analyze foraging distances and frequencies. SNH and OSR reduced foraging distance at different spatial scales and depending on season, with possible benefits for the performance of honey bee colonies. Frequency of pollen foragers per habitat type was equally high for SNH, grassland and OSR fields, but lower for other crops and forest. In landscapes with a small proportion of SNH a significantly higher density of pollen foragers on SNH was observed, indicating the limitation of pollen resources in simple agricultural landscapes and the importance of SNH. 6. Quantity and diversity of collected pollen can influence the growth and health of honey bee colonies, but little is known about the influence of landscape structure on pollen diet. In a field experiment we rotated 16 honey bee colonies across 16 agricultural landscapes (see also Chapter 5), used traps to get samples of collected pollen and observed the intra-colonial dance communication to gain information about foraging distances. Neither the amount of collected pollen nor pollen diversity were related to landscape diversity. The revealed increase of foraging distances with decreasing landscape diversity suggests that honey bees compensate for a lower landscape diversity by increasing their pollen foraging range in order to maintain pollen amount and diversity. 7. Our results show the importance of diverse pollen resources for honey bee colonies in agricultural landscapes. Beside the risk of exposure to pesticides honey bees face the risk of nutritional deficiency with implications for their health. By modifying landscape composition and therefore availability of resources we are able to contribute to the wellbeing of honey bees. Agri-environmental schemes aiming to support pollinators should focus on possible spatial and temporal gaps in pollen availability and diversity in agricultural landscapes.}, subject = {Apis mellifera}, language = {en} } @phdthesis{Daniels1999, author = {Daniels, Justin John Douglas}, title = {Interaction of Salmonella typhimurium and Listeria monocytogenes with the murine host}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1073}, school = {Universit{\"a}t W{\"u}rzburg}, year = {1999}, abstract = {Food borne pathogens that cause systemic disease must cross the intestinal barrier. Many of these pathogens, eg Salmonella typhimurium and Shigella flexneri, use M cells, found only within the follicle associated epithelium (FAE) that overlies Peyer's patches and other lymphoid follicles, to enter the host. This study is primarily an investigation into the interaction of S. typhimurium and Listeria monocytogenes with the intestinal epithelium, representing the early stage of an infection.}, subject = {Maus}, language = {en} } @article{DanielTraenknerWojtaszetal.2014, author = {Daniel, Katrin and Tr{\"a}nkner, Daniel and Wojtasz, Lukasz and Shibuya, Hiroki and Watanabe, Yoshinori and Alsheimer, Manfred and Toth, Attila}, title = {Mouse CCDC79 (TERB1) is a meiosis-specific telomere associated protein}, series = {BMC Cell Biology}, volume = {15}, journal = {BMC Cell Biology}, number = {17}, issn = {1471-2121}, doi = {10.1186/1471-2121-15-17}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-116248}, year = {2014}, abstract = {Background: Telomeres have crucial meiosis-specific roles in the orderly reduction of chromosome numbers and in ensuring the integrity of the genome during meiosis. One such role is the attachment of telomeres to trans-nuclear envelope protein complexes that connect telomeres to motor proteins in the cytoplasm. These trans-nuclear envelope connections between telomeres and cytoplasmic motor proteins permit the active movement of telomeres and chromosomes during the first meiotic prophase. Movements of chromosomes/telomeres facilitate the meiotic recombination process, and allow high fidelity pairing of homologous chromosomes. Pairing of homologous chromosomes is a prerequisite for their correct segregation during the first meiotic division. Although inner-nuclear envelope proteins, such as SUN1 and potentially SUN2, are known to bind and recruit meiotic telomeres, these proteins are not meiosis-specific, therefore cannot solely account for telomere-nuclear envelope attachment and/or for other meiosis-specific characteristics of telomeres in mammals. Results: We identify CCDC79, alternatively named TERB1, as a meiosis-specific protein that localizes to telomeres from leptotene to diplotene stages of the first meiotic prophase. CCDC79 and SUN1 associate with telomeres almost concurrently at the onset of prophase, indicating a possible role for CCDC79 in telomere-nuclear envelope interactions and/or telomere movements. Consistent with this scenario, CCDC79 is missing from most telomeres that fail to connect to SUN1 protein in spermatocytes lacking the meiosis-specific cohesin SMC1B. SMC1B-deficient spermatocytes display both reduced efficiency in telomere-nuclear envelope attachment and reduced stability of telomeres specifically during meiotic prophase. Importantly, CCDC79 associates with telomeres in SUN1-deficient spermatocytes, which strongly indicates that localization of CCDC79 to telomeres does not require telomere-nuclear envelope attachment. Conclusion: CCDC79 is a meiosis-specific telomere associated protein. Based on our findings we propose that CCDC79 plays a role in meiosis-specific telomere functions. In particular, we favour the possibility that CCDC79 is involved in telomere-nuclear envelope attachment and/or the stabilization of meiotic telomeres. These conclusions are consistent with the findings of an independently initiated study that analysed CCDC79/TERB1 functions.}, language = {en} } @article{DandekarTollervey1992, author = {Dandekar, Thomas and Tollervey, David}, title = {Mutational analysis of Schizosaccharomyces pombe U4 snRNA by plasmid exchange}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29969}, year = {1992}, abstract = {No abstract available}, language = {en} } @article{DandekarTollervey1989, author = {Dandekar, Thomas and Tollervey, David}, title = {Cloning of Schizosaccharomyces pombe genes encoding the U1,U2,U3 and U4 snRNAs}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29919}, year = {1989}, abstract = {No abstract available}, language = {en} } @article{DandekarTollervey1993, author = {Dandekar, Thomas and Tollervey, David}, title = {Identification and functional analysis of a novel yeast small nucleolar RNA}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29850}, year = {1993}, abstract = {No abstract available}, language = {en} } @article{DandekarTollervey1991, author = {Dandekar, Thomas and Tollervey, D.}, title = {Thirty-three nucleotides of 5' flanking sequence including the TATA box are necessary and sufficient for efficient U2 snRNA transcription in Schizosaccharomycespombe}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29959}, year = {1991}, abstract = {No abstract available}, language = {en} } @article{DandekarStripeckeGrayetal.1991, author = {Dandekar, Thomas and Stripecke, Renata and Gray, Nicola K. and Goossen, Britta and Constable, Anne and Johansson, Hans E. and Hentze, Matthias W.}, title = {Identification of a novel iron-responsive element in murine and human erythroid \(\delta\)-aminolevulinic acid synthase mRNA}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29929}, year = {1991}, abstract = {No abstract available}, language = {en} } @article{DandekarSibbald1990, author = {Dandekar, Thomas and Sibbald, Peter R.}, title = {Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29798}, year = {1990}, abstract = {No abstract available}, language = {en} } @article{DandekarSchulz1987, author = {Dandekar, Thomas and Schulz, R.}, title = {Evidence for the expression of peptides derived from three opioid precursors in NG 108CC15 hybrid cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29909}, year = {1987}, abstract = {No abstract available}, language = {en} } @article{DandekarRibesTollervey1989, author = {Dandekar, Thomas and Ribes, V. and Tollervey, David}, title = {Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29771}, year = {1989}, abstract = {No abstract available}, language = {en} } @article{DandekarLiangKrueger2013, author = {Dandekar, Thomas and Liang, Chunguang and Kr{\"u}ger, Beate}, title = {GoSynthetic database tool to analyse natural and engineered molecular processes}, series = {Database}, journal = {Database}, doi = {10.1093/database/bat043}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-97023}, year = {2013}, abstract = {An essential topic for synthetic biologists is to understand the structure and function of biological processes and involved proteins and plan experiments accordingly. Remarkable progress has been made in recent years towards this goal. However, efforts to collect and present all information on processes and functions are still cumbersome. The database tool GoSynthetic provides a new, simple and fast way to analyse biological processes applying a hierarchical database. Four different search modes are implemented. Furthermore, protein interaction data, cross-links to organism-specific databases (17 organisms including six model organisms and their interactions), COG/KOG, GO and IntAct are warehoused. The built in connection to technical and engineering terms enables a simple switching between biological concepts and concepts from engineering, electronics and synthetic biology. The current version of GoSynthetic covers more than one million processes, proteins, COGs and GOs. It is illustrated by various application examples probing process differences and designing modifications.}, language = {en} } @article{DandekarGramschHoughtonetal.1985, author = {Dandekar, Thomas and Gramsch, Christian and Houghton, Richard A. and Schultz, R{\"u}diger}, title = {Affinity purification of \(\beta\)-endorphin-like material from NG108CC15 cells by means of the monoclonal \(\beta\)-endorphin antibody 3-E7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29896}, year = {1985}, abstract = {No abstract available}, language = {en} } @article{DandekarFieselmannPoppetal.2012, author = {Dandekar, Thomas and Fieselmann, Astrid and Popp, Jasmin and Hensel, Michael}, title = {Salmonella enterica: a surprisingly well-adapted intracellular lifestyle}, series = {Frontiers in Microbiology}, journal = {Frontiers in Microbiology}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123135}, year = {2012}, abstract = {The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole (SCV) in host cells. We summarize latest results on metabolic requirements for Salmonella during infection. This includes intracellular phenotypes of mutant strains based on metabolic modeling and experimental tests, isotopolog profiling using (13)C-compounds in intracellular Salmonella, and complementation of metabolic defects for attenuated mutant strains towards a comprehensive understanding of the metabolic requirements of the intracellular lifestyle of Salmonella. Helpful for this are also genomic comparisons. We outline further recent studies and which analyses of intracellular phenotypes and improved metabolic simulations were done and comment on technical required steps as well as progress involved in the iterative refinement of metabolic flux models, analyses of mutant phenotypes, and isotopolog analyses. Salmonella lifestyle is well-adapted to the SCV and its specific metabolic requirements. Salmonella metabolism adapts rapidly to SCV conditions, the metabolic generalist Salmonella is quite successful in host infection.}, language = {en} } @article{DandekarFieselmannFischeretal.2014, author = {Dandekar, Thomas and Fieselmann, Astrid and Fischer, Eva and Popp, Jasmin and Hensel, Michael and Noster, Janina}, title = {Salmonella—how a metabolic generalist adopts an intracellular lifestyle during infection}, series = {Frontiers in Cellular and Infection Microbiology}, volume = {4}, journal = {Frontiers in Cellular and Infection Microbiology}, number = {191}, issn = {2235-2988}, doi = {10.3389/fcimb.2014.00191}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120686}, year = {2014}, abstract = {The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, "-omics" data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.}, language = {en} } @article{DandekarFieselmannFischeretal.2015, author = {Dandekar, Thomas and Fieselmann, Astrid and Fischer, Eva and Popp, Jasmin and Hensel, Michael and Noster, Janina}, title = {Salmonella - how a metabolic generalist adopts an intracellular lifestyle during infection}, series = {Frontiers in Cellular and Infection Microbiology}, volume = {4}, journal = {Frontiers in Cellular and Infection Microbiology}, number = {191}, doi = {10.3389/fcimb.2014.00191}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-149029}, year = {2015}, abstract = {The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, "-omics" data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.}, language = {en} } @article{DandekarEisenreich2015, author = {Dandekar, Thomas and Eisenreich, Wolfgang}, title = {Host-adapted metabolism and its regulation in bacterial pathogens}, series = {Frontiers in Cellular and Infection Microbiology}, volume = {5}, journal = {Frontiers in Cellular and Infection Microbiology}, number = {28}, issn = {2235-2988}, doi = {10.3389/fcimb.2015.00028}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-196876}, year = {2015}, abstract = {No abstract available.}, language = {en} } @article{DandekarArgos1994, author = {Dandekar, Thomas and Argos, Patrick}, title = {Amiloride-sensitive epithelial Na\(^+\) channel is made of three homologous subunits}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29734}, year = {1994}, abstract = {No abstract available}, language = {en} } @misc{DandekarArgos1992, author = {Dandekar, Thomas and Argos, Patrick}, title = {A novel heterodimeric cysteine protease is required for interleukin 1ß processing in monocytes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29986}, year = {1992}, abstract = {No abstract available}, language = {en} } @misc{DandekarArgos1992, author = {Dandekar, Thomas and Argos, Patrick}, title = {Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29814}, year = {1992}, abstract = {No abstract available}, language = {en} } @misc{DandekarArgos1991, author = {Dandekar, Thomas and Argos, Patrick}, title = {Chaperonin-mediated protein folding at the surface of groEL through a "molten globule" intermediate}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29939}, year = {1991}, abstract = {No abstract available}, language = {en} } @inproceedings{DandekarArgos1993, author = {Dandekar, Thomas and Argos, P.}, title = {Genetic algorithms as a new tool to study protein stability}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29990}, year = {1993}, abstract = {No abstract available}, language = {en} } @misc{DandekarArgos1993, author = {Dandekar, Thomas and Argos, P.}, title = {Drug assay using antibody mimics made by molecular imprinting}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-30003}, year = {1993}, abstract = {No abstract available}, language = {en} } @misc{DandekarArgos1994, author = {Dandekar, Thomas and Argos, P.}, title = {Three-dimensional structure of the 67k N-terminal Fragment of E.coli DNA Topoisomerase I}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29836}, year = {1994}, abstract = {No abstract available}, language = {en} } @misc{DandekarArgos1993, author = {Dandekar, Thomas and Argos, P.}, title = {The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted \(\alpha\)-helices: Crystal structure of the protein DNA-complex}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29866}, year = {1993}, abstract = {No abstract available}, language = {en} } @article{DandekarAhmedSamanetal.2013, author = {Dandekar, Thomas and Ahmed, Zeeshan and Saman, Zeeshan and Huber, Claudia and Hensel, Michael and Schomburg, Dietmar and M{\"u}nch, Richard and Eisenreich, Wolfgang}, title = {Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling}, series = {BMC Bioinformatics}, journal = {BMC Bioinformatics}, doi = {10.1186/1471-2334-13-266}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-95882}, year = {2013}, abstract = {Background The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. Results The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. Conclusions The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.}, language = {en} } @unpublished{Dandekar2019, author = {Dandekar, Thomas}, title = {Biological heuristics applied to cosmology suggests a condensation nucleus as start of our universe and inflation cosmology replaced by a period of rapid Weiss domain-like crystal growth}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-183945}, pages = {24}, year = {2019}, abstract = {Cosmology often uses intricate formulas and mathematics to derive new theories and concepts. We do something different in this paper: We look at biological processes and derive from these heuristics so that the revised cosmology agrees with astronomical observations but does also agree with standard biological observations. We show that we then have to replace any type of singularity at the start of the universe by a condensation nucleus and that the very early period of the universe usually assumed to be inflation has to be replaced by a period of rapid crystal growth as in Weiss magnetization domains. Impressively, these minor modifications agree well with astronomical observations including removing the strong inflation perturbations which were never observed in the recent BICEP2 experiments. Furthermore, looking at biological principles suggests that such a new theory with a condensation nucleus at start and a first rapid phase of magnetization-like growth of the ordered, physical laws obeying lattice we live in is in fact the only convincing theory of the early phases of our universe that also is compatible with current observations. We show in detail in the following that such a process of crystal creation, breaking of new crystal seeds and ultimate evaporation of the present crystal readily leads over several generations to an evolution and selection of better, more stable and more self-organizing crystals. Moreover, this explains the "fine-tuning" question why our universe is fine-tuned to favor life: Our Universe is so self-organizing to have enough offspring and the detailed physics involved is at the same time highly favorable for all self-organizing processes including life. This biological theory contrasts with current standard inflation cosmologies. The latter do not perform well in explaining any phenomena of sophisticated structure creation or self-organization. As proteins can only thermodynamically fold by increasing the entropy in the solution around them we suggest for cosmology a condensation nucleus for a universe can form only in a "chaotic ocean" of string-soup or quantum foam if the entropy outside of the nucleus rapidly increases. We derive an interaction potential for 1 to n-dimensional strings or quantum-foams and show that they allow only 1D, 2D, 4D or octonion interactions. The latter is the richest structure and agrees to the E8 symmetry fundamental to particle physics and also compatible with the ten dimensional string theory E8 which is part of the M-theory. Interestingly, any other interactions of other dimensionality can be ruled out using Hurwitz compositional theorem. Crystallization explains also extremely well why we have only one macroscopic reality and where the worldlines of alternative trajectories exist: They are in other planes of the crystal and for energy reasons they crystallize mostly at the same time, yielding a beautiful and stable crystal. This explains decoherence and allows to determine the size of Planck´s quantum h (very small as separation of crystal layers by energy is extremely strong). Ultimate dissolution of real crystals suggests an explanation for dark energy agreeing with estimates for the "big rip". The halo distribution of dark matter favoring galaxy formation is readily explained by a crystal seed starting with unit cells made of normal and dark matter. That we have only matter and not antimatter can be explained as there may be right handed mattercrystals and left-handed antimatter crystals. Similarly, real crystals are never perfect and we argue that exactly such irregularities allow formation of galaxies, clusters and superclusters. Finally, heuristics from genetics suggest to look for a systems perspective to derive correct vacuum and Higgs Boson energies.}, 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 }, language = {en} } @misc{Dandekar1991, author = {Dandekar, Thomas}, title = {Yeast U3 localization and correct sequence (snR17a) and promotor activity (snR17b) identified by homology search}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29781}, year = {1991}, abstract = {No abstract available}, language = {en} } @unpublished{Dandekar2021, author = {Dandekar, Thomas}, title = {Our universe may have started by Qubit decoherence}, doi = {10.25972/OPUS-23918}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239181}, pages = {54}, year = {2021}, abstract = {Our universe may have started by Qubit decoherence: In quantum computers, qubits have all their states undefined during calculation and become defined as output ("decoherence"). We study the transition from an uncontrolled, chaotic quantum vacuum ("before") to a clearly interacting "real world". In such a cosmology, the Big Bang singularity is replaced by a condensation event of interacting strings. This triggers a crystallization process. This avoids inflation, not fitting current observations: increasing long-range interactions limit growth and crystal symmetries ensure the same laws of nature and basic symmetries over the whole crystal. Tiny mis-arrangements provide nuclei of superclusters and galaxies and crystal structure allows arrangement of dark (halo regions) and normal matter (galaxy nuclei) for galaxy formation. Crystals come and go: an evolutionary cosmology is explored: entropic forces from the quantum soup "outside" of the crystal try to dissolve it. This corresponds to dark energy and leads to a "big rip" in 70 Gigayears. Selection for best growth and condensation events over generations of crystals favors multiple self-organizing processes within the crystal including life or even conscious observers in our universe. Philosophically this theory shows harmony with nature and replaces absurd perspectives of current cosmology. Independent of cosmology, we suggest that a "real world" (so our everyday macroscopic world) happens only inside a crystal. "Outside" there is wild quantum foam and superposition of all possibilities. In our crystallized world the vacuum no longer boils but is cooled down by the crystallization event, space-time exists and general relativity holds. Vacuum energy becomes 10**20 smaller, exactly as observed in our everyday world. We live in a "solid" state, within a crystal, the n quanta which build our world have all their different m states nicely separated. There are only nm states available for this local "multiverse". The arrow of entropy for each edge of the crystal forms one fate, one world-line or clear development of our world, while layers of the crystal are different system states. Mathematical leads from loop quantum gravity (LQG) point to required interactions and potentials. Interaction potentials for strings or loop quanta of any dimension allow a solid, decoherent state of quanta challenging to calculate. However, if we introduce here the heuristic that any type of physical interaction of strings corresponds just to a type of calculation, there is already since 1898 the Hurwitz theorem showing that then only 1D, 2D, 4D and 8D (octonions) allow complex or hypercomplex number calculations. No other hypercomplex numbers and hence dimensions or symmetries are possible to allow calculations without yielding divisions by zero. However, the richest solution allowed by the Hurwitz theorem, octonions, is actually the observed symmetry of our universe, E8. Standard physics such as condensation, crystallization and magnetization but also solid-state physics and quantum computing allow us to show an initial mathematical treatment of our new theory by LQG to describe the cosmological state transformations by equations, and, most importantly, point out routes to parametrization of free parameters looking at testable phenomena, experiments and formulas that describe processes of crystallization, protein folding, magnetization, solid-state physics and quantum computing. This is presented here for LQG, for string theory it would be more elegant but was too demanding to be shown here. Note: While my previous Opus server preprint "A new cosmology of a crystallization process (decoherence) from the surrounding quantum soup provides heuristics to unify general relativity and quantum physics by solid state physics" (https://doi.org/10.25972/OPUS-23076) deals with the same topics and basic formulas, this new version is improved: clearer in title, better introduction, more stringent in its mathematics and improved discussion of the implications including quantum computing, hints for parametrization and connections to LQG and other current cosmological efforts. This 5th of June 2021 version is again an OPUS preprint, but this will next be edited for Archives https://arxiv.org.}, language = {en} } @unpublished{Dandekar2008, author = {Dandekar, Thomas}, title = {Why are nature´s constants so fine-tuned? The case for an escalating complex universe}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-34488}, year = {2008}, abstract = {Why is our universe so fine-tuned? In this preprint we discuss that this is not a strange accident but that fine-tuned universes can be considered to be exceedingly large if one counts the number of observable different states (i.e. one aspect of the more general preprint http://www.opus-bayern.de/uni-wuerzburg/volltexte/2009/3353/). Looking at parameter variation for the same set of physical laws simple and complex processes (including life) and worlds in a multiverse are compared in simple examples. Next the anthropocentric principle is extended as many conditions which are generally interpreted anthropocentric only ensure a large space of different system states. In particular, the observed over-tuning beyond the level for our existence is explainable by these system considerations. More formally, the state space for different systems becomes measurable and comparable looking at their output behaviour. We show that highly interacting processes are more complex then Chaitin complexity, the latter denotes processes not compressible by shorter descriptions (Kolomogorov complexity). The complexity considerations help to better study and compare different processes (programs, living cells, environments and worlds) including dynamic behaviour and can be used for model selection in theoretical physics. Moreover, the large size (in terms of different states) of a world allowing complex processes including life can in a model calculation be determined applying discrete histories from quantum spin-loop theory. Nevertheless there remains a lot to be done - hopefully the preprint stimulates further efforts in this area.}, subject = {Natur}, language = {en} } @misc{Dandekar1991, author = {Dandekar, Thomas}, title = {Olbers' Paradox (peer-reviewed scientific correspondence)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-31672}, year = {1991}, abstract = {No abstract available}, language = {en} } @unpublished{Dandekar2023, author = {Dandekar, Thomas}, title = {A modified inflation cosmology relying on qubit-crystallization: rare qubit interactions trigger qubit ensemble growth and crystallization into "real" bit-ensembles and emergent time}, doi = {10.25972/OPUS-32177}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-321777}, pages = {42}, year = {2023}, abstract = {In a modified inflation scenario we replace the "big bang" by a condensation event in an eternal all-compassing big ocean of free qubits in our modified cosmology. Interactions of qubits in the qubit ocean are rare. If they happen, they provide a nucleus for a new universe as the qubits become decoherent and freeze-out into defined bit ensembles. Second, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth) - the crystal unit cell guarantees same symmetries everywhere. Hence, the textbook inflation scenario to explain the same laws of nature in our domain is replaced by the crystal unit cell of the crystal formed. We give here only the perspective or outline of this modified inflation theory, as the detailed mathematical physics behind this has still to be formulated and described. Interacting qubits solidify, quantum entropy decreases (but increases in the ocean around). The interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, but more importantly can explain well by such a type of cosmological crystallization instead of inflation the early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: no annihilation of antimatter necessary, rather the unit cell of our crystal universe has a matter handedness avoiding anti-matter. We prove a triggering of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, this means that in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below h dash liquidity left). However, the E8 symmetry of heterotic string theory has six rolled-up, small dimensions which help to keep the qubit crystal together and will never expand. Finally, we give first energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field in the crystal. Hence, vacuum energy gets low inside the qubit crystal. Condensed mathematics may advantageously help to model free (many states denote the same qubit) and bound qubits in phase space.}, language = {en} } @unpublished{Dandekar2024, author = {Dandekar, Thomas}, title = {How do qubits interact? Implications for fundamental physics}, doi = {10.25972/OPUS-35743}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-357435}, pages = {42}, year = {2024}, abstract = {Proteins fold in water and achieve a clear structure despite a huge parameter space. Inside a (protein) crystal you have everywhere the same symmetries as there is everywhere the same unit cell. We apply this to qubit interactions to do fundamental physics: We modify cosmological inflation: we replace the big bang by a condensation event in an eternal all-encompassing ocean of free qubits. Rare interactions of qubits in the ocean provide a nucleus or seed for a new universe (domain), as the qubits become decoherent and freeze-out into defined bit ensembles. Next, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth). The crystal unit cell guarantees same symmetries (and laws of nature) everywhere inside the crystal, no inflation scenario is needed. Interacting qubits solidify, quantum entropy decreases in the crystal, but increases outside in the ocean. The interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After this very early modified steps, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements. Applying the Hurwitz theorem to qubits we prove that initiation of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. We describe a six-bit-ensemble toy model of qubit interaction and the repulsive forces of qubits for ultra-short distances. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below Planck´s quantum is liquidity left). The E8 symmetry of heterotic string theory has six curled-up, small dimensions. These keep the qubit crystal together and never expand. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit crystal formation. Implications are fundamental answers, e.g. why there is fine-tuning for life-friendliness, why there is string theory with rolled-up dimension and so many free parameters. We explain by cosmological crystallization instead of inflation the early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: the unit cell of our crystal universe has a matter handedness avoiding anti-matter. Importantly, crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. Vacuum energy gets appropriate low inside the crystal by its qubit binding energy, outside it is 10**20 higher. Scalar fields for color interaction/confinement and gravity could be derived from the qubit-interaction field.}, language = {en} } @unpublished{Dandekar2023, author = {Dandekar, Thomas}, title = {Protein folding and crystallization applied to qubit interactions and fundamental physics yields a modified inflation model for cosmology}, doi = {10.25972/OPUS-34615}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346156}, pages = {42}, year = {2023}, abstract = {Protein folding achieves a clear solution structure in a huge parameter space (the so-called protein folding problem). Proteins fold in water, and get by this a highly ordered structure. Finally, inside a protein crystal for structure resolution, you have everywhere the same symmetries as there is everywhere the same unit cell. We apply this to qubit interactions to do fundamental physics: in a modified cosmology, we replace the big bang by a condensation event in an eternal all-encompassing ocean of free qubits. Interactions of qubits in the qubit ocean are quite rare but provide a nucleus or seed for a new universe (domain) as the qubits become decoherent and freeze-out into defined bit ensembles. Second, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth). The crystal unit cell guarantees same symmetries everywhere inside the crystal. The textbook inflation scenario to explain the same laws of nature in our domain is replaced by the unit cell of the crystal formed. Interacting qubits solidify, quantum entropy decreases (but increases in the ocean around). In a modified inflation scenario, the interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. Then standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements. We explain by cosmological crystallization instead of inflation: early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: the unit cell of our crystal universe has a matter handedness avoiding anti-matter. We prove initiation of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below Planck quantum there is liquidity left). The E8 symmetry of heterotic string theory has six curled-up, small dimensions which help to keep the qubit crystal together and will never expand. Mathematics focusses on the Hurwitz proof applied to qubit interaction, a toy model of qubit interaction and repulsive forces of qubits. Vacuum energy gets appropriate low inside the crystal. We give first energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction/confinement and gravity are derived from the qubit-interaction field.}, language = {en} } @unpublished{Dandekar2023, author = {Dandekar, Thomas}, title = {Analysing the phase space of the standard model and its basic four forces from a qubit phase transition perspective: implications for large-scale structure generation and early cosmological events}, doi = {10.25972/OPUS-29858}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-298580}, pages = {42}, year = {2023}, abstract = {The phase space for the standard model of the basic four forces for n quanta includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. We replace the "big bang" by a condensation event (interacting qubits become decoherent) and inflation by a crystallization event - the crystal unit cell guarantees same symmetries everywhere. Interacting qubits solidify and form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, large-scale structure of voids and filaments, supercluster formation, galaxy formation, dominance of matter and life-friendliness. We prove qubit interactions to be 1,2,4 or 8 dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field. Hence, vacuum energy gets low only inside the qubit crystal. Condensed mathematics may advantageously model free / bound qubits in phase space.}, language = {en} } @unpublished{Dandekar2022, author = {Dandekar, Thomas}, title = {Qubit transition into defined Bits: A fresh perspective for cosmology and unifying theories}, doi = {10.25972/OPUS-26641}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-266418}, pages = {42}, year = {2022}, abstract = {In this view point we do not change cosmology after the hot fireball starts (hence agrees well with observation), but the changed start suggested and resulting later implications lead to an even better fit with current observations (voids, supercluster and galaxy formation; matter and no antimatter) than the standard model with big bang and inflation: In an eternal ocean of qubits, a cluster of qubits crystallizes to defined bits. The universe does not jump into existence ("big bang") but rather you have an eternal ocean of qubits in free super-position of all their quantum states (of any dimension, force field and particle type) as permanent basis. The undefined, boiling vacuum is the real "outside", once you leave our everyday universe. A set of n Qubits in the ocean are "liquid", in very undefined state, they have all their m possibilities for quantum states in free superposition. However, under certain conditions the qubits interact, become defined, and freeze out, crystals form and give rise to a defined, real world with all possible time series and world lines. GR holds only within the crystal. In our universe all n**m quantum possibilities are nicely separated and crystallized out to defined bit states: A toy example with 6 qubits each having 2 states illustrates, this is completely sufficient to encode space using 3 bits for x,y and z, 1 bit for particle type and 2 bits for its state. Just by crystallization, space, particles and their properties emerge from the ocean of qubits, and following the arrow of entropy, time emerges, following an arrow of time and expansion from one corner of the toy universe to everywhere else. This perspective provides time as emergent feature considering entropy: crystallization of each world line leads to defined world lines over their whole existence, while entropy ensures direction of time and higher representation of high entropy states considering the whole crystal and all slices of world lines. The crystal perspective is also economic compared to the Everett-type multiverse, each qubit has its m quantum states and n qubits interacting forming a crystal and hence turning into defined bit states has only n**m states and not more states. There is no Everett-type world splitting with every decision but rather individual world trajectories reside in individual world layers of the crystal. Finally, bit-separated crystals come and go in the qubit ocean, selecting for the ability to lay seeds for new crystals. This self-organizing reproduction selects over generations also for life-friendliness. Mathematical treatment introduces quantum action theory as a framework for a general lattice field theory extending quantum chromo dynamics where scalar fields for color interaction and gravity have to be derived from the permeating qubit-interaction field. Vacuum energy should get appropriately low by the binding properties of the qubit crystal. Connections to loop quantum gravity, string theory and emergent gravity are discussed. Standard physics (quantum computing; crystallization, solid state physics) allow validation tests of this perspective and will extend current results.}, language = {en} } @techreport{Dandekar2021, type = {Working Paper}, author = {Dandekar, Thomas}, title = {A new cosmology of a crystallization process (decoherence) from the surrounding quantum soup provides heuristics to unify general relativity and quantum physics by solid state physics}, doi = {10.25972/OPUS-23076}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230769}, pages = {42 Seiten}, year = {2021}, abstract = {We explore a cosmology where the Big Bang singularity is replaced by a condensation event of interacting strings. We study the transition from an uncontrolled, chaotic soup ("before") to a clearly interacting "real world". Cosmological inflation scenarios do not fit current observations and are avoided. Instead, long-range interactions inside this crystallization event limit growth and crystal symmetries ensure the same laws of nature and basic symmetries over our domain. Tiny mis-arrangements present nuclei of superclusters and galaxies and crystal structure leads to the arrangement of dark (halo regions) and normal matter (galaxy nuclei) so convenient for galaxy formation. Crystals come and go, allowing an evolutionary cosmology where entropic forces from the quantum soup "outside" of the crystal try to dissolve it. These would correspond to dark energy and leads to a big rip scenario in 70 Gy. Preference of crystals with optimal growth and most condensation nuclei for the next generation of crystals may select for multiple self-organizing processes within the crystal, explaining "fine-tuning" of the local "laws of nature" (the symmetry relations formed within the crystal, its "unit cell") to be particular favorable for self-organizing processes including life or even conscious observers in our universe. Independent of cosmology, a crystallization event may explain quantum-decoherence in general: The fact, that in our macroscopic everyday world we only see one reality. This contrasts strongly with the quantum world where you have coherence, a superposition of all quantum states. We suggest that a "real world" (so our everyday macroscopic world) happens only in our domain, i.e. inside a crystal. "Outside" of our domain and our observable universe there is the quantum soup of boiling quantum foam and superposition of all possibilities. In our crystallized world the vacuum no longer boils but is cooled down by the crystallization event and hence is 10**20 smaller, exactly as observed in our everyday world. As we live in a "solid" state, within a crystal, the different quanta which build our world have all their different states nicely separated. This theory postulates there are only n quanta and m states available for them (there is no Everett-like ever splitting multiverse after each decision). In the solid state we live in, there is decoherence, the states are nicely separated. The arrow of entropy for each edge of the crystal forms one fate, one worldline or clear development of a world, while the layers of the crystal are different system states. Some mathematical leads from loop quantum gravity point to required interactions and potentials. A complete mathematical treatment of this unified theory is far too demanding currently. Interaction potentials for strings or membranes of any dimension allow a solid state of quanta, so allowing decoherence in our observed world are challenging to calculate. However, if we introduce here the heuristic that any type of physical interaction of strings corresponds just to a type of calculation, there is already since 1898 the Hurwitz theorem showing that then only 1D, 2D, 4D and 8D (octonions) allow complex or hypercomplex number calculations. No other hypercomplex numbers and hence dimensions or symmetries are possible to allow calculations without yielding divisions by zero. However, the richest solution allowed by the Hurwitz theorem, octonions, is actually the observed symmetry of our universe, E8.  }, subject = {Kosmologie}, language = {en} }