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Isothermal titration calorimetry (ITC) is a widely used technique for the characterization of protein-protein and protein-ligand interactions. It provides information on the stoichiometry, affinity, and the thermodynamic driving forces of interactions. This chapter exemplifies the use of ITC to investigate interactions between human autophagy modifiers (LC3/GABARAP proteins) and their interaction partners, the LIR motif containing sequences. The purpose of this report is to present a detailed protocol for the production of LC3/GABARAP-interacting LIR peptides using E. coli expression systems. In addition, we outline the design of ITC experiments using the LC3/GABARAP:peptide interactions as an example. Comprehensive troubleshooting notes are provided to facilitate the adaptation of these protocols to different ligand-receptor systems. The methodology outlined for studying protein-ligand interactions will help to avoid common errors and misinterpretations of experimental results.
Der interdisziplinäre Sammelband eröffnet neue Perspektiven auf den Stil als bislang unterkonturierte literaturwissenschaftliche Leitkategorie unter transnationalen, wissens-, gattungs- und sprachgeschichtlichen Gesichtspunkten. Im 18. Jahrhundert zeichnet sich im Nachdenken über Schreibarten eine Neujustierung der Stilkategorie ab, die den Stil zur Reflexionsgröße für ästhetische Diskurse macht. Der Band sondiert die Pluralisierung, Historisierung und Individualisierung der Stilkategorie, die ihr neue literatur- und kulturtheoretische Anwendungsbereiche eröffnet. Die Bewegungen zwischen den Sprachen, Literaturen, Medien und semantischen Feldern erschließt die Publikation, indem sie europäische Vergleichshorizonte eröffnet und literatur- ebenso wie sprachwissenschaftliche Ansätze präsentiert. Damit leistet sie einen Beitrag zum Feld der komparatistisch ausgerichteten Germanistik, insbesondere der Literatur- und Kulturgeschichte des 18. Jahrhunderts und des europäischen Kulturtransfers.
The total charm-quark production cross section per unit of rapidity dσ(cc)/dy, and the fragmentation fractions of charm quarks to different charm-hadron species f(c → hc), are measured for the first time in p–Pb collisions at √sNN = 5.02 TeV at midrapidity (−0.96 < y < 0.04 in the centre-ofmass frame) using data collected by ALICE at the CERN LHC. The results are obtained based on all the available measurements of prompt production of ground-state charm-hadron species: D0, D+,D+s, and J/ψ mesons, and Λ+cand Ξ0cbaryons. The resulting cross section is dσ(cc)/dy = 219.6±6.3 (stat.)+10.5−11.8(syst.)+7.6−2.9(extr.)±5.4 (BR)±4.6 (lumi.)±19.5 (rapidity shape) +15.0 (Ω0c) mb, which is consistent with a binary scaling of pQCD calculations from pp ollisions. The measured fragmentation fractions are compatible with those measured in pp collisions at √s = 5.02 and 13 TeV, showing an increase in the relative production rates of charm baryons with respect to charm mesons in pp and p–Pb collisions compared with e+e − and e−p collisions. The pT-integrated nuclear modification factor of charm quarks, RpPb(cc) = 0.91±0.04 (stat.) +0.08 −0.09 (syst.) +0.04 −0.03 (extr.)±0.03 (lumi.), is found to be consistent with unity and with theoretical predictions including nuclear modifications of the parton distribution functions.
Natural Language Processing (NLP) for big data requires an efficient and sophisticated infrastructure to complete tasks both fast and correctly. Providing an intuitive and lightweight interaction with a framework that abstracts and simplifies complex tasks assists in reaching this goal. This bachelor thesis extends the NLP framework Docker Unified UIMA Interface (DUUI) by an API and a web-based graphical user interface to control and manage pipelines for automated analysis of large quantities of natural language. The extension aims to reduce the entry barrier into the field as well as to accelerate the creation and management of pipelines according to UIMA standards. Pipelines can be executed in the browser or using the web API directly and then monitored on a document level. The evaluation in usability and user experience indicates that the implementation benefits the framework by making its usage more user friendly, lightweight, and intuitive while also making the management of pipelines more efficient.
The e+e−→D+sDs1(2536)− and e+e−→D+sD∗s2(2573)− processes are studied using data samples collected with the BESIII detector at center-of-mass energies from 4.530 to 4.946~GeV. The absolute branching fractions of Ds1(2536)−→D¯∗0K− and D∗s2(2573)−→D¯0K− are measured for the first time to be (35.9±4.8±3.5)% and (37.4±3.1±4.6)%, respectively. The measurements are in tension with predictions based on the assumption that the Ds1(2536) and D∗s2(2573) are dominated by a bare cs¯ component. The e+e−→D+sDs1(2536)− and e+e−→D+sD∗s2(2573)− cross sections are measured, and a resonant structure at around 4.6~GeV with a width of 50~MeV is observed for the first time with a statistical significance of 15σ in the e+e−→D+sD∗s2(2573)− process. It could be the Y(4626) found by the Belle collaboration in the D+sDs1(2536)− final state, since they have similar masses and widths. There is also evidence for a structure at around 4.75~GeV in both processes.
Dass das ZfL ihn seit Kurzem als Senior Fellow führt, passt so gar nicht zu der ungestümen Neugierde und den kreativen Energien, die sich Detlev Schöttker nicht nur bewahrt hat, sondern die jüngst über der Beschäftigung mit einem neuen Gegenstand eine neue Qualität gewonnen haben. Instantan, vehement und bedingungslos hat er sich nach dem Umzug des ZfL nach Wilmersdorf in ein neues Forschungsprojekt weniger vertieft als gestürzt. Doch recht besehen ist es kein neuer Gegenstand, sondern es sind seine alten Bekannten, die ihm rund um den Fasanenplatz wiederbegegnen. Ein größeres Geschenk als diese Nachbarschaft hätte man ihm vielleicht nicht machen können: Die literarische und kulturelle Moderne entstand hier! Der Fasanenplatz ist ein 'Freilichtmuseum' der Moderne mit Hauptmann, Brecht, Benjamin und vielen anderen. Und Detlev Schöttker wäre nicht Detlev Schöttker, wenn er die Öffentlichkeit nicht sogleich über einige seiner Funde und Entdeckungen informiert hätte. In der FAZ sind bereits mehrere Artikel von ihm über die erstaunliche Bedeutung unseres Kiezes für die Moderne erschienen.
Das Fach "Allgemeine und vergleichende Literaturwissenschaft (AVL)" beschäftigt sich mit dem Vergleich von Literatur aus verschiedenen Kulturen, Epochen und Gattungen. Der Begriff "Komparatistik" wird weitgehend synonym verwendet, legt aber einen noch stärkeren Schwerpunkt auf den Vergleich als allgemeine epistemologische Praxis, vor dem der Fokus auf Literatur in den Hintergrund geraten kann. Die Geschichte des Fachs in Deutschland reicht bis in das 19. Jahrhundert zurück, in dem es - in etwa zeitgleich mit den "Nationalphilologien" (hier also Germanistik) - vor allem im Sinne einer vergleichenden Literaturgeschichte entstand. Während in den Anfängen Einflussforschung und Gattungsgeschichte im Vordergrund standen, hat das Fach im 20. Jahrhundert mehrere Ausweitungen erfahren. So zählen beispielsweise auch die allgemeine Literatur- und Kulturtheorie, die Ästhetik und der Vergleich von Literatur mit anderen Medien zu den Forschungsgebieten der AVL. Schon früh wurde der grenzüberschreitende Anspruch der AVL über den von J.W. Goethe lancierten Begriff "Weltliteratur" bestimmt. Entsprechend gehört auch die Frage, wie der Begriff historisch verstanden wurde und wie er im Zeitalter beschleunigter Globalisierung zu denken ist, zu den prominentesten Debatten im Rahmen der AVL. In der ursprünglichen Konzeption von Goethe war "Weltliteratur" als Dialog zwischen den Nationalliteraturen gedacht, wobei sowohl Rezeption (des kulturell Fremden) als auch Widerspiegelung (des Eigenen in der Rezeption durch Andere) im Vordergrund standen. Heute wird die eurozentrische Orientierung des Begriffs problematisiert, aber die Frage bleibt virulent, ob und wie Literatur aus verschiedenen Kulturen und Sprachen auf eine universelle Ebene gehoben werden kann, ohne ihre spezifischen Kontexte zu verlieren.
Als Carlo Ginzburg die These formulierte, dass die Geisteswissenschaften wie die Kriminalliteratur im sog. "Indizienparadigma" gründeten, hatte er mit Sherlock Holmes einen Detektiv vor Augen, der persönlich den Tatort besichtigte. Dort erhob er Spuren, kombinierte sie und kam in oftmals ingeniösen, aber auch höchst spekulativen Schlussfolgerungen zur Lösung seines Falls. Vor dem Hintergrund aktueller Entwicklungen in Forschung und Fahndung muss dieses materiell und empirisch grundierte "Indizienparadigma" jedoch einer Revision unterzogen werden. Denn seit der Privatdetektiv von "Kommissar Computer" Konkurrenz bekommen hat, haben sich die Investigationspraktiken grundlegend gewandelt: So können computergestützte Fahndungs- und Aufklärungsmethoden eine Besichtigung des Tatorts ersetzen, während algorithmische Wahrscheinlichkeitsrechnung vergangene wie zukünftige Fälle erhellt. Der vorliegende Sammelband mit Beiträgen aus der Literatur-, Medien- und Designwissenschaft untersucht, inwiefern solche "virtuellen Investigationen" in Literatur und Kunst der Gegenwart eine Revision des Indizienparadigmas einschließen - und inwiefern Begriffe der Virtualität bereits die Investigativarbeit im 19. Jahrhundert prägten.
The family of cubic noncentrosymmetric 3-4-3 compounds has become a fertile ground for the discovery of novel correlated metallic and insulating phases. Here, we report the synthesis of a new heavy fermion compound, Ce3Bi4Ni3. It is an isoelectronic analog of the prototypical Kondo insulator Ce3Bi4Pt3 and of the recently discovered Weyl-Kondo semimetal Ce3Bi4Pd3. In contrast to the volume-preserving Pt-Pd substitution, structural and chemical analyses reveal a positive chemical pressure effect in Ce3Bi4Ni3 relative to its heavier counterparts. Based on the results of electrical resistivity, Hall effect, magnetic susceptibility, and specific heat measurements, we identify an energy gap of 65-70 meV, about eight times larger than that in Ce3Bi4Pt3 and about 45 times larger than that of the Kondo-insulating background hosting the Weyl nodes in Ce3Bi4Pd3. We show that this gap as well as other physical properties do not evolve monotonically with increasing atomic number, i.e., in the sequence Ce3Bi4Ni3-Ce3Bi4Pd3-Ce3Bi4Pt3, but instead with increasing partial electronic density of states of the d orbitals at the Fermi energy. To understand under which condition topological states form in these materials is a topic for future studies.
Heterostructures of graphene in proximity to magnetic insulators open the possibility to investigate exotic states emerging from the interplay of magnetism, strain and charge transfer between the layers. Recent reports on the growth of self-integrated atomic wires of β-RuCl3 on graphite suggest these materials as versatile candidates to investigate these effects. Here we present detailed first principles calculations on the charge transfer and electronic structure of β-RuCl3/heterostructures and provide a comparison with the work function analysis of the related honeycomb family members α-RuX3 (X = Cl,Br,I). We find that proximity of the two layers leads to a hole-doped graphene and electron-doped RuX3 in all cases, which is sensitively dependent on the distance between the two layers. Furthermore, strain effects due to lattice mismatch control the magnetization which itself has a strong effect on the charge transfer. Charge accumulation in β-RuCl3 strongly drops away from the chain making such heterostructures suitable candidates for sharp interfacial junctions in graphene-based devices.
canning tunneling microscopy (STM) is perhaps the most promising way to detect the superconducting gap size and structure in the canonical unconventional superconductor Sr2RuO4 directly. However, in many cases, researchers have reported being unable to detect the gap at all in simple STM conductance measurements. Recently, an investigation of this issue on various local topographic structures on a Sr-terminated surface found that superconducting spectra appeared only in the region of small nanoscale canyons, corresponding to the removal of one RuO surface layer. Here, we analyze the electronic structure of various possible surface structures using first principles methods, and argue that bulk conditions favorable for superconductivity can be achieved when removal of the RuO layer suppresses the RuO4 octahedral rotation locally. We further propose alternative terminations to the most frequently reported Sr termination where superconductivity surfaces should be observed.
Motivated by recently reported magnetic-field induced topological phases in ultracold atoms and correlated Moiré materials, we investigate topological phase transitions in a minimal model consisting of interacting spinless fermions described by the Hofstadter model on a square lattice. For interacting lattice Hamiltonians in the presence of a commensurate magnetic flux it has been demonstrated that the quantized Hall conductivity is constrained by a Lieb-Schultz-Mattis (LSM)-type theorem due to magnetic translation symmetry. In this work, we revisit the validity of the theorem for such models and establish that a topological phase transition from a topological to a trivial insulating phase can be realized but must be accompanied by spontaneous magnetic translation symmetry breaking caused by charge ordering of the spinless fermions. To support our findings, the topological phase diagram for varying interaction strength is mapped out numerically with exact diagonalization for different flux quantum ratios and band fillings using symmetry indicators. We discuss our results in the context of the LSM-type theorem.
On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)
(2024)
This study explores the potential of a novel genome-wide association study (GWAS) approach for identifying loci underlying quantitative polygenic traits in natural populations. Extensive population genetic forward simulations demonstrate that the approach is generally effective for oligogenic and moderately polygenic traits and relatively insensitive to low heritability, but applicability is limited for highly polygenic architectures and pronounced population structure. The required sample size is moderate with very good results being obtained already for a few dozen populations scored. The method performs well in predicting population means even with a moderate false positive rate. When combined with machine learning for feature selection, this rate can be further reduced. The data efficiency of the method, particularly when using pooled sequencing, makes GWAS studies more accessible for research in biodiversity genomics. Overall, this study highlights the promise of this popGWAS approach for dissecting the genetic basis of complex traits in natural populations.
Motivated by the on-going discussion on the nature of magnetism in the quantum Ising chain CoNb2O6, we present a first-principles-based analysis of its exchange interactions by applying an \textit{ab initio} approach with additional modelling that accounts for various drawbacks of a purely density functional theory ansatz. With this method we are able to extract and understand the origin of the magnetic couplings under inclusion of all symmetry-allowed terms, and to resolve the conflicting model descriptions in CoNb2O6. We find that the twisted Kitaev chain and the transverse-field ferromagnetic Ising chain views are mutually compatible, although additional off-diagonal exchanges are necessary to provide a complete picture. We show that the dominant exchange interaction is a ligand-centered exchange process - involving the eg electrons -, which is rendered anisotropic by the low-symmetry crystal fields environments in CoNb2O6, giving rise to the dominant Ising exchange, while the smaller bond-dependent anisotropies are found to originate from d−d kinetic exchange processes involving the t2g electrons. We demonstrate the validity of our approach by comparing the predictions of the obtained low-energy model to measured THz and inelastic neutron scattering spectra.
he family of cubic noncentrosymmetric 3-4-3 compounds has become a fertile ground for the discovery of novel correlated metallic and insulating phases. Here, we report the synthesis of a new heavy fermion compound, Ce3Bi4Ni3. It is an isoelectronic analog of the prototypical Kondo insulator Ce3Bi4Pt3 and of the recently discovered Weyl-Kondo semimetal Ce3Bi4Pd3. In contrast to the volume-preserving Pt-Pd substitution, structural and chemical analyses reveal a positive chemical pressure effect in Ce3Bi4Ni3 relative to its heavier counterparts. Based on the results of electrical resistivity, Hall effect, magnetic susceptibility, and specific heat measurements, we identify an energy gap of 65–70 meV, about eight times larger than that in Ce3Bi4Pt3 and about 45 times larger than that of the Kondo-insulating background hosting the Weyl nodes in Ce3Bi4Pd3. We show that this gap as well as other physical properties do not evolve monotonically with increasing atomic number, i.e., in the sequence Ce3Bi4Ni3−Ce3Bi4Pd3−Ce3Bi4Pt3, but instead with increasing partial electronic density of states of the 𝑑 orbitals at the Fermi energy. This work opens the possibility to investigate the conditions under which topological states develop in this series of strongly correlated 3-4-3 materials.
Abstract
Seed harvesting from wild plant populations is key for ecological restoration, but may threaten the persistence of source populations. Consequently, several countries have set guidelines limiting the proportions of harvestable seeds. However, these guidelines are so far inconsistent, and they lack a solid empirical basis. Here, we use high-resolution data from 298 plant species to model the demographic consequences of seed harvesting. We find that the current guidelines do not protect populations of annuals and short-lived perennials, while they are overly restrictive for long-lived plants. We show that the maximum possible fraction of seed production – what can be harvested without compromising the long-term persistence of populations – is strongly related to the generation time of the target species. When harvesting every year, this safe seed fraction ranges from 80% in long-lived species to 2% in most annuals. Less frequent seed harvesting substantially increases the safe seed fraction: In the most vulnerable annual species, it is safe to harvest 5%, 10% or 30% of population seed production when harvesting every two, five or ten years, respectively. Our results provide a quantitative basis for seed harvesting legislations worldwide, based on species’ generation time and harvesting regime.
Significance The UN Decade on Ecosystem Restoration, 2021-2030, foresees upscaling restoration, and the demand for native seed is skyrocketing. Seeds for restoring native vegetation are often harvested in wild, but too intensive harvest can threaten the donor populations. Existing guidelines that set limits to wild seed harvest are mostly based on expert opinions, yet they commonly lack empirical basis and vary among regions in one order of magnitude. We show that the current guidelines urgently need to be reformulated, because they are overly restrictive in long-lived species, while they do not protect annual plants from extinction. Using matrix population models of nearly 300 plant species, we provide a quantitative basis for a new seed harvesting legislation world-wide.
Dynamic imaging of landmark organelles, such as nuclei, cell membrane, nuclear envelope, and lipid droplets enables image-based phenotyping of functional states of cells. Multispectral fluorescent imaging of landmark organelles requires labor-intensive labeling, limits throughput, and compromises cell health. Virtual staining of label-free images with deep neural networks is an emerging solution for this problem. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining saves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Published approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. This paper reports model training protocols for virtual staining of nuclei and membranes robust to label-free imaging parameters, cell states, and cell types. We developed a flexible and scalable convolutional architecture, named UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including neuromasts of zebrafish, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and membranes. The models rescue the missing label, non-uniform expression of labels, and photobleaching. We share three pre-trained models, named VSCyto3D, VSCyto2D, and VSNeuromast, as well as VisCy, a PyTorch-based pipeline for training, inference, and deployment that leverages the modern OME-Zarr format.
Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth
(2024)
Clb2 is a conserved mitotic B-type cyclin, the levels of which are finely controlled to drive progression through the cell cycle. While it is known that CLB2 transcription and Clb2 protein degradation are important for precise control of its expression, it remains unclear whether the synthesis of Clb2 is also regulated. To address whether and how Clb2 expression levels respond to cell growth changes and adapt cell cycle progression, we combined single-cell and single-molecule imaging methods to measure CLB2 mRNA and protein expression throughout the Saccharomyces cerevisiae cell cycle. We found that the CLB2 mRNA was efficiently localized to the yeast bud as soon as this compartment was formed, but strikingly the Clb2 protein accumulated in the mother nucleus. The CLB2 mRNA localization in the yeast bud by the She2-3 complex did not control protein localization but rather promoted CLB2 translation. Moreover, CLB2 mRNA bud localization and protein synthesis were coupled and dependent on a single secondary structure -a ZIP code-located in the coding sequence. In a CLB2 ZIP code mutant, mRNA localization was impaired and Clb2 protein synthesis decreased, resulting in changes in cell cycle distribution and increased size of daughter cells at birth. Finally, while in WT cells the Clb2 protein concentration followed bud growth, this relationship was impaired in the ZIP code mutant. We propose that S. cerevisiae couples the control of CLB2 mRNA bud localization and protein synthesis to coordinate cell growth and cell cycle progression. This mechanism extends our knowledge of CLB2 expression regulation, and constitutes a novel function for mRNA localization.
Highlights
• The 1986 Immigration Reform and Control Act legalized millions of Hispanic migrants.
• The IRCA receive significantly increases state-to-county fiscal transfers.
• Electoral incentives of the state governor drive the fiscal response of the IRCA.
• Legalization increases Hispanic turnout and political engagement.
Abstract
We study the impact of immigrant legalization on fiscal transfers from state to local governments in the United States, exploiting variation in legal status from the 1986 Immigration Reform and Control Act (IRCA). State governments allocate more resources to IRCA counties, an allocation that is responsive to the electoral incentives of the governor. Importantly, the effect emerges prior to the enfranchisement of the IRCA migrants and we argue it is driven by the IRCA’s capacity to politically empower already legal Hispanic migrants in mixed legal status communities. The IRCA increases turnout in large Hispanic communities as well as Hispanic political engagement, without detectably triggering anti-migrant sentiment.