TY - INPR A1 - Dandekar, Thomas T1 - A modified inflation cosmology relying on qubit-crystallization: rare qubit interactions trigger qubit ensemble growth and crystallization into “real” bit-ensembles and emergent time N2 - 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. KW - qubit KW - cosmology KW - decoherence KW - crystallization KW - emergent time Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-321777 ER - TY - RPRT A1 - Dandekar, Thomas T1 - 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 T1 - Eine neue Kosmologie eines Kristallisationsprozesses (Dekohärenz) vom umgebenden Quantenschaum bietet Heuristiken, um allgemeine Relativitätstheorie und Quantenphysik durch Festkörperphysik zu vereinen N2 - 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.   KW - Kosmologie KW - cosmology KW - Hurwitz-Theorem KW - Quantenschleifen-Gravitation KW - Verschränkung KW - Qubits KW - Hurwitz-Theorem KW - loop quantum gravity KW - entanglement KW - Qubits Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230769 ER - TY - JOUR A1 - Dandekar, Thomas A1 - Argos, Patrick T1 - A novel heterodimeric cysteine protease is required for interleukin 1ß processing in monocytes N2 - No abstract available Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-29986 ER - TY - JOUR A1 - Rackevei, Antonia S. A1 - Borges, Alyssa A1 - Engstler, Markus A1 - Dandekar, Thomas A1 - Wolf, Matthias T1 - About the analysis of 18S rDNA sequence data from trypanosomes in barcoding and phylogenetics: tracing a continuation error occurring in the literature JF - Biology N2 - The variable regions (V1–V9) of the 18S rDNA are routinely used in barcoding and phylogenetics. In handling these data for trypanosomes, we have noticed a misunderstanding that has apparently taken a life of its own in the literature over the years. In particular, in recent years, when studying the phylogenetic relationship of trypanosomes, the use of V7/V8 was systematically established. However, considering the current numbering system for all other organisms (including other Euglenozoa), V7/V8 was never used. In Maia da Silva et al. [Parasitology 2004, 129, 549–561], V7/V8 was promoted for the first time for trypanosome phylogenetics, and since then, more than 70 publications have replicated this nomenclature and even discussed the benefits of the use of this region in comparison to V4. However, the primers used to amplify the variable region of trypanosomes have actually amplified V4 (concerning the current 18S rDNA numbering system). KW - RNA secondary structure KW - variable regions KW - V1–V9 KW - V4 KW - V7/V8 KW - Trypanosoma Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-297562 SN - 2079-7737 VL - 11 IS - 11 ER - TY - JOUR A1 - Dandekar, Thomas A1 - Gramsch, Christian A1 - Houghton, Richard A. A1 - Schultz, Rüdiger T1 - Affinity purification of \(\beta\)-endorphin-like material from NG108CC15 cells by means of the monoclonal \(\beta\)-endorphin antibody 3-E7 N2 - No abstract available Y1 - 1985 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-29896 ER - TY - JOUR A1 - Gupta, Shishir K. A1 - Srivastava, Mugdha A1 - Minocha, Rashmi A1 - Akash, Aman A1 - Dangwal, Seema A1 - Dandekar, Thomas T1 - Alveolar regeneration in COVID-19 patients: a network perspective JF - International Journal of Molecular Sciences N2 - A viral infection involves entry and replication of viral nucleic acid in a host organism, subsequently leading to biochemical and structural alterations in the host cell. In the case of SARS-CoV-2 viral infection, over-activation of the host immune system may lead to lung damage. Albeit the regeneration and fibrotic repair processes being the two protective host responses, prolonged injury may lead to excessive fibrosis, a pathological state that can result in lung collapse. In this review, we discuss regeneration and fibrosis processes in response to SARS-CoV-2 and provide our viewpoint on the triggering of alveolar regeneration in coronavirus disease 2019 (COVID-19) patients. KW - COVID-19 KW - SARS-CoV-2 KW - alveolar regeneration KW - alveolar fibrosis KW - signaling pathway KW - network biology Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-284307 SN - 1422-0067 VL - 22 IS - 20 ER - TY - JOUR A1 - Dandekar, Thomas A1 - Argos, Patrick T1 - Amiloride-sensitive epithelial Na\(^+\) channel is made of three homologous subunits N2 - No abstract available Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-29734 ER - TY - JOUR A1 - Breitenbach, Tim A1 - Helfrich-Förster, Charlotte A1 - Dandekar, Thomas T1 - An effective model of endogenous clocks and external stimuli determining circadian rhythms JF - Scientific Reports N2 - Circadian endogenous clocks of eukaryotic organisms are an established and rapidly developing research field. To investigate and simulate in an effective model the effect of external stimuli on such clocks and their components we developed a software framework for download and simulation. The application is useful to understand the different involved effects in a mathematical simple and effective model. This concerns the effects of Zeitgebers, feedback loops and further modifying components. We start from a known mathematical oscillator model, which is based on experimental molecular findings. This is extended with an effective framework that includes the impact of external stimuli on the circadian oscillations including high dose pharmacological treatment. In particular, the external stimuli framework defines a systematic procedure by input-output-interfaces to couple different oscillators. The framework is validated by providing phase response curves and ranges of entrainment. Furthermore, Aschoffs rule is computationally investigated. It is shown how the external stimuli framework can be used to study biological effects like points of singularity or oscillators integrating different signals at once. The mathematical framework and formalism is generic and allows to study in general the effect of external stimuli on oscillators and other biological processes. For an easy replication of each numerical experiment presented in this work and an easy implementation of the framework the corresponding Mathematica files are fully made available. They can be downloaded at the following link: https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/circadian/. KW - computational biology and bioinformatics KW - systems biology Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-261655 VL - 11 IS - 1 ER - TY - JOUR A1 - Alnusaire, Taghreed S. A1 - Sayed, Ahmed M. A1 - Elmaidomy, Abeer H. A1 - Al-Sanea, Mohammad M. A1 - Albogami, Sarah A1 - Albqmi, Mha A1 - Alowaiesh, Bassam F. A1 - Mostafa, Ehab M. A1 - Musa, Arafa A1 - Youssif, Khayrya A. A1 - Refaat, Hesham A1 - Othman, Eman M. A1 - Dandekar, Thomas A1 - Alaaeldin, Eman A1 - Ghoneim, Mohammed M. A1 - Abdelmohsen, Usama Ramadan T1 - An in vitro and in silico study of the enhanced antiproliferative and pro-oxidant potential of Olea europaea L. cv. Arbosana leaf extract via elastic nanovesicles (spanlastics) JF - Antioxidants N2 - The olive tree is a venerable Mediterranean plant and often used in traditional medicine. The main aim of the present study was to evaluate the effect of Olea europaea L. cv. Arbosana leaf extract (OLE) and its encapsulation within a spanlastic dosage form on the improvement of its pro-oxidant and antiproliferative activity against HepG-2, MCF-7, and Caco-2 human cancer cell lines. The LC-HRESIMS-assisted metabolomic profile of OLE putatively annotated 20 major metabolites and showed considerable in vitro antiproliferative activity against HepG-2, MCF-7, and Caco-2 cell lines with IC\(_{50}\) values of 9.2 ± 0.8, 7.1 ± 0.9, and 6.5 ± 0.7 µg/mL, respectively. The encapsulation of OLE within a (spanlastic) nanocarrier system, using a spraying method and Span 40 and Tween 80 (4:1 molar ratio), was successfully carried out (size 41 ± 2.4 nm, zeta potential 13.6 ± 2.5, and EE 61.43 ± 2.03%). OLE showed enhanced thermal stability, and an improved in vitro antiproliferative effect against HepG-2, MCF-7, and Caco-2 (IC\(_{50}\) 3.6 ± 0.2, 2.3 ± 0.1, and 1.8 ± 0.1 µg/mL, respectively) in comparison to the unprocessed extract. Both preparations were found to exhibit pro-oxidant potential inside the cancer cells, through the potential inhibitory activity of OLE against glutathione reductase and superoxide dismutase (IC\(_{50}\) 1.18 ± 0.12 and 2.33 ± 0.19 µg/mL, respectively). These inhibitory activities were proposed via a comprehensive in silico study to be linked to the presence of certain compounds in OLE. Consequently, we assume that formulating such a herbal extract within a suitable nanocarrier would be a promising improvement of its therapeutic potential. KW - olive KW - metabolomic profiling KW - antiproliferative KW - pro-oxidant KW - encapsulation KW - spanlastic KW - nanocarrier KW - docking KW - molecular dynamics simulation KW - Olea Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-250064 SN - 2076-3921 VL - 10 IS - 12 ER - TY - JOUR A1 - Li, Kunkun A1 - Prada, Juan A1 - Damineli, Daniel S. C. A1 - Liese, Anja A1 - Romeis, Tina A1 - Dandekar, Thomas A1 - Feijó, José A. A1 - Hedrich, Rainer A1 - Konrad, Kai Robert T1 - An optimized genetically encoded dual reporter for simultaneous ratio imaging of Ca\(^{2+}\) and H\(^{+}\) reveals new insights into ion signaling in plants JF - New Phytologist N2 - Whereas the role of calcium ions (Ca\(^{2+}\)) in plant signaling is well studied, the physiological significance of pH‐changes remains largely undefined. Here we developed CapHensor, an optimized dual‐reporter for simultaneous Ca\(^{2+}\) and pH ratio‐imaging and studied signaling events in pollen tubes (PTs), guard cells (GCs), and mesophyll cells (MCs). Monitoring spatio‐temporal relationships between membrane voltage, Ca\(^{2+}\)‐ and pH‐dynamics revealed interconnections previously not described. In tobacco PTs, we demonstrated Ca\(^{2+}\)‐dynamics lag behind pH‐dynamics during oscillatory growth, and pH correlates more with growth than Ca\(^{2+}\). In GCs, we demonstrated abscisic acid (ABA) to initiate stomatal closure via rapid cytosolic alkalization followed by Ca2+ elevation. Preventing the alkalization blocked GC ABA‐responses and even opened stomata in the presence of ABA, disclosing an important pH‐dependent GC signaling node. In MCs, a flg22‐induced membrane depolarization preceded Ca2+‐increases and cytosolic acidification by c. 2 min, suggesting a Ca\(^{2+}\)/pH‐independent early pathogen signaling step. Imaging Ca2+ and pH resolved similar cytosol and nuclear signals and demonstrated flg22, but not ABA and hydrogen peroxide to initiate rapid membrane voltage‐, Ca\(^{2+}\)‐ and pH‐responses. We propose close interrelation in Ca\(^{2+}\)‐ and pH‐signaling that is cell type‐ and stimulus‐specific and the pH having crucial roles in regulating PT growth and stomata movement. KW - abscisic acid (ABA) KW - calcium KW - flg22 KW - guard cells KW - imaging KW - ion signaling KW - pH KW - pollen tube Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-239847 VL - 230 IS - 6 SP - 2292 EP - 2310 ER -