@article{11462, abstract = {Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens.}, author = {Dormeshkin, Dmitri and Shapira, Michail and Karputs, Alena and Kavaleuski, Anton and Kuzminski, Ivan and Stepanova, Elena and Gilep, Andrei}, issn = {1432-0614}, journal = {Applied Microbiology and Biotechnology}, pages = {5093--5103}, publisher = {Springer Nature}, title = {{Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development}}, doi = {10.1007/s00253-022-12022-w}, volume = {106}, year = {2022}, } @article{11469, abstract = {Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization.}, author = {Brighi, Pietro and Michailidis, Alexios and Kirova, Kristina and Abanin, Dmitry A. and Serbyn, Maksym}, issn = {2469-9969}, journal = {Physical Review B}, number = {22}, publisher = {American Physical Society}, title = {{Localization of a mobile impurity interacting with an Anderson insulator}}, doi = {10.1103/physrevb.105.224208}, volume = {105}, year = {2022}, } @article{11470, abstract = {Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.}, author = {Brighi, Pietro and Michailidis, Alexios A. and Abanin, Dmitry A. and Serbyn, Maksym}, issn = {2469-9969}, journal = {Physical Review B}, number = {22}, publisher = {American Physical Society}, title = {{Propagation of many-body localization in an Anderson insulator}}, doi = {10.1103/physrevb.105.l220203}, volume = {105}, year = {2022}, } @article{11471, abstract = {Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. }, author = {Sack, Stefan and Medina Ramos, Raimel A and Michailidis, Alexios and Kueng, Richard and Serbyn, Maksym}, issn = {2691-3399}, journal = {PRX Quantum}, keywords = {General Medicine}, number = {2}, publisher = {American Physical Society}, title = {{Avoiding barren plateaus using classical shadows}}, doi = {10.1103/prxquantum.3.020365}, volume = {3}, year = {2022}, } @phdthesis{11473, abstract = {The polaron model is a basic model of quantum field theory describing a single particle interacting with a bosonic field. It arises in many physical contexts. We are mostly concerned with models applicable in the context of an impurity atom in a Bose-Einstein condensate as well as the problem of electrons moving in polar crystals. The model has a simple structure in which the interaction of the particle with the field is given by a term linear in the field’s creation and annihilation operators. In this work, we investigate the properties of this model by providing rigorous estimates on various energies relevant to the problem. The estimates are obtained, for the most part, by suitable operator techniques which constitute the principal mathematical substance of the thesis. The first application of these techniques is to derive the polaron model rigorously from first principles, i.e., from a full microscopic quantum-mechanical many-body problem involving an impurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas in the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak interactions as a low-energy effective theory for this problem. In the second part, we investigate rigorously the ground state of the model at fixed momentum and for large values of the coupling constant. Qualitatively, the system is expected to display a transition from the quasi-particle behavior at small momenta, where the dispersion relation is parabolic and the particle moves through the medium dragging along a cloud of phonons, to the radiative behavior at larger momenta where the polaron decelerates and emits free phonons. At the same time, in the strong coupling regime, the bosonic field is expected to behave purely classically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to be asymptotically equal to the one obtained from the semiclassical counterpart of the problem, first studied by Landau and Pekar in the 1940s. For polaron models with regularized form factors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear function of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove that for a large window of momenta below the radiation threshold, the energy-momentum relation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the Landau–Pekar effective mass, as expected. For the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is of the optical type and the form factor is formally UV–singular due to the nature of the point charge-dipole interaction, we are able to give the corresponding upper bound. In contrast to the regular case, this requires the inclusion of the quantum fluctuations of the phonon field, which makes the problem considerably more difficult. The results are supplemented by studies on the absolute ground-state energy at strong coupling, a proof of the divergence of the effective mass with the coupling constant for a wide class of polaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model and the application of the techniques used for its removal for the energy estimates. }, author = {Mysliwy, Krzysztof}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Polarons in Bose gases and polar crystals: Some rigorous energy estimates}}, doi = {10.15479/at:ista:11473}, year = {2022}, } @inproceedings{11476, abstract = {Messaging platforms like Signal are widely deployed and provide strong security in an asynchronous setting. It is a challenging problem to construct a protocol with similar security guarantees that can efficiently scale to large groups. A major bottleneck are the frequent key rotations users need to perform to achieve post compromise forward security. In current proposals – most notably in TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft) – for users in a group of size n to rotate their keys, they must each craft a message of size log(n) to be broadcast to the group using an (untrusted) delivery server. In larger groups, having users sequentially rotate their keys requires too much bandwidth (or takes too long), so variants allowing any T≤n users to simultaneously rotate their keys in just 2 communication rounds have been suggested (e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates are either damaging or expensive (or both); i.e. they either result in future operations being more costly (e.g. via “blanking” or “tainting”) or are costly themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20]. In this paper we propose CoCoA; a new scheme that allows for T concurrent updates that are neither damaging nor costly. That is, they add no cost to future operations yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock et al.] lower bound, CoCoA increases the number of rounds needed to complete all updates from 2 up to (at most) log(n); though typically fewer rounds are needed. The key insight of our protocol is the following: in the (non-concurrent version of) TreeKEM, a delivery server which gets T concurrent update requests will approve one and reject the remaining T−1. In contrast, our server attempts to apply all of them. If more than one user requests to rotate the same key during a round, the server arbitrarily picks a winner. Surprisingly, we prove that regardless of how the server chooses the winners, all previously compromised users will recover after at most log(n) such update rounds. To keep the communication complexity low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly forwards packets, but instead actively computes individualized packets tailored to each user. As the server is untrusted, this change requires us to develop new mechanisms ensuring robustness of the protocol.}, author = {Alwen, Joël and Auerbach, Benedikt and Cueto Noval, Miguel and Klein, Karen and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z and Walter, Michael}, booktitle = {Advances in Cryptology – EUROCRYPT 2022}, isbn = {9783031070846}, issn = {1611-3349}, location = {Trondheim, Norway}, pages = {815–844}, publisher = {Springer Nature}, title = {{CoCoA: Concurrent continuous group key agreement}}, doi = {10.1007/978-3-031-07085-3_28}, volume = {13276}, year = {2022}, } @article{11478, abstract = {Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain.}, author = {Bartalska, Katarina and Hübschmann, Verena and Korkut, Medina and Cubero, Ryan J and Venturino, Alessandro and Rössler, Karl and Czech, Thomas and Siegert, Sandra}, issn = {2589-0042}, journal = {iScience}, number = {7}, publisher = {Elsevier}, title = {{A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation}}, doi = {10.1016/j.isci.2022.104580}, volume = {25}, year = {2022}, } @article{11489, abstract = {Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.}, author = {Bilanovičová, V and Rýdza, N and Koczka, L and Hess, M and Feraru, E and Friml, Jiří and Nodzyński, T}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, number = {11}, pages = {6352}, publisher = {MDPI}, title = {{The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein}}, doi = {10.3390/ijms23116352}, volume = {23}, year = {2022}, } @misc{11542, author = {Schulz, Rouven}, publisher = {Institute of Science and Technology Austria}, title = {{Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)}}, doi = {10.15479/AT:ISTA:11542}, year = {2022}, } @article{11545, abstract = {We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings. We show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category N have the structure of highest weight categories and we establish a BGG reciprocity theorem for N .}, author = {Brown, Adam and Romanov, Anna}, issn = {0021-8693}, journal = {Journal of Algebra}, keywords = {Algebra and Number Theory}, number = {11}, pages = {145--179}, publisher = {Elsevier}, title = {{Contravariant pairings between standard Whittaker modules and Verma modules}}, doi = {10.1016/j.jalgebra.2022.06.017}, volume = {609}, year = {2022}, } @article{11546, abstract = {Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.}, author = {Westram, Anja M and Faria, Rui and Johannesson, Kerstin and Butlin, Roger and Barton, Nicholas H}, issn = {1471-2970}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology}, number = {1856}, publisher = {Royal Society of London}, title = {{Inversions and parallel evolution}}, doi = {10.1098/rstb.2021.0203}, volume = {377}, year = {2022}, } @article{11551, abstract = {Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.}, author = {Molina-Granada, David and González-Vioque, Emiliano and Dibley, Marris G. and Cabrera-Pérez, Raquel and Vallbona-Garcia, Antoni and Torres-Torronteras, Javier and Sazanov, Leonid A and Ryan, Michael T. and Cámara, Yolanda and Martí, Ramon}, issn = {23993642}, journal = {Communications Biology}, number = {1}, publisher = {Springer Nature}, title = {{Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit}}, doi = {10.1038/s42003-022-03568-6}, volume = {5}, year = {2022}, } @article{11552, abstract = {Rotational dynamics of D2 molecules inside helium nanodroplets is induced by a moderately intense femtosecond pump pulse and measured as a function of time by recording the yield of HeD+ ions, created through strong-field dissociative ionization with a delayed femtosecond probe pulse. The yield oscillates with a period of 185 fs, reflecting field-free rotational wave packet dynamics, and the oscillation persists for more than 500 periods. Within the experimental uncertainty, the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier analysis, is the same as Bgas for an isolated D2 molecule. Our observations show that the D2 molecules inside helium nanodroplets essentially rotate as free D2 molecules.}, author = {Qiang, Junjie and Zhou, Lianrong and Lu, Peifen and Lin, Kang and Ma, Yongzhe and Pan, Shengzhe and Lu, Chenxu and Jiang, Wenyu and Sun, Fenghao and Zhang, Wenbin and Li, Hui and Gong, Xiaochun and Averbukh, Ilya Sh and Prior, Yehiam and Schouder, Constant A. and Stapelfeldt, Henrik and Cherepanov, Igor and Lemeshko, Mikhail and Jäger, Wolfgang and Wu, Jian}, issn = {10797114}, journal = {Physical Review Letters}, number = {24}, publisher = {American Physical Society}, title = {{Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets}}, doi = {10.1103/PhysRevLett.128.243201}, volume = {128}, year = {2022}, } @article{11553, abstract = {In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is: • To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues. • To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics. • Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are: • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS; • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009); • the QC-Criterion and the Spreading Principle from KSS. The purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings. • To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings: • puzzle pieces shrink to points, • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate. • We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings are the analogues of Lattès maps in this setting. • We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.}, author = {Clark, Trevor and Drach, Kostiantyn and Kozlovski, Oleg and Strien, Sebastian Van}, issn = {2199-6806}, journal = {Arnold Mathematical Journal}, number = {2}, pages = {319--410}, publisher = {Springer Nature}, title = {{The dynamics of complex box mappings}}, doi = {10.1007/s40598-022-00200-7}, volume = {8}, year = {2022}, } @article{11556, abstract = {We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the oscillations with respect to fluctuations and noise.}, author = {Kalinov, Aleksei and Osinskiy, A.I. and Matveev, S.A. and Otieno, W. and Brilliantov, N.V.}, issn = {0021-9991}, journal = {Journal of Computational Physics}, keywords = {Computer Science Applications, Physics and Astronomy (miscellaneous), Applied Mathematics, Computational Mathematics, Modeling and Simulation, Numerical Analysis}, publisher = {Elsevier}, title = {{Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics}}, doi = {10.1016/j.jcp.2022.111439}, volume = {467}, year = {2022}, } @article{11587, abstract = {Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. Results: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. Conclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.}, author = {Zhang, Runxuan and Kuo, Richard and Coulter, Max and Calixto, Cristiane P.G. and Entizne, Juan Carlos and Guo, Wenbin and Marquez, Yamile and Milne, Linda and Riegler, Stefan and Matsui, Akihiro and Tanaka, Maho and Harvey, Sarah and Gao, Yubang and Wießner-Kroh, Theresa and Paniagua, Alejandro and Crespi, Martin and Denby, Katherine and Hur, Asa Ben and Huq, Enamul and Jantsch, Michael and Jarmolowski, Artur and Koester, Tino and Laubinger, Sascha and Li, Qingshun Quinn and Gu, Lianfeng and Seki, Motoaki and Staiger, Dorothee and Sunkar, Ramanjulu and Szweykowska-Kulinska, Zofia and Tu, Shih Long and Wachter, Andreas and Waugh, Robbie and Xiong, Liming and Zhang, Xiao Ning and Conesa, Ana and Reddy, Anireddy S.N. and Barta, Andrea and Kalyna, Maria and Brown, John W.S.}, issn = {1474-760X}, journal = {Genome Biology}, publisher = {BioMed Central}, title = {{A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis}}, doi = {10.1186/s13059-022-02711-0}, volume = {23}, year = {2022}, } @article{11588, abstract = {Visualizing cell behavior and effector function on a single cell level has been crucial for understanding key aspects of mammalian biology. Due to their small size, large number and rapid recruitment into thrombi, there is a lack of data on fate and behavior of individual platelets in thrombosis and hemostasis. Here we report the use of platelet lineage restricted multi-color reporter mouse strains to delineate platelet function on a single cell level. We show that genetic labeling allows for single platelet and megakaryocyte (MK) tracking and morphological analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven Confetti expression, we provide insights into temporal gene expression patterns as well as spatial clustering of MK in the bone marrow. In the vasculature, shape analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia formation with no evidence of lamellipodia formation. Single cell tracking in complex thrombi reveals prominent myosin-dependent motility of platelets and highlights thrombus formation as a highly dynamic process amenable to modification and intervention of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry, as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions of multicolor reporter mice compared to wild-type controls. In conclusion, platelet lineage multicolor reporter mice prove useful in furthering our understanding of platelet and MK biology on a single cell level.}, author = {Nicolai, Leo and Kaiser, Rainer and Escaig, Raphael and Hoffknecht, Marie Louise and Anjum, Afra and Leunig, Alexander and Pircher, Joachim and Ehrlich, Andreas and Lorenz, Michael and Ishikawa-Ankerhold, Hellen and Aird, William C. and Massberg, Steffen and Gärtner, Florian R}, issn = {1592-8721}, journal = {Haematologica}, number = {7}, pages = {1669--1680}, publisher = {Ferrata Storti Foundation}, title = {{Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo}}, doi = {10.3324/haematol.2021.278896}, volume = {107}, year = {2022}, } @article{11589, abstract = {Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.}, author = {Wang, Ren and Himschoot, Ellie and Chen, Jian and Boudsocq, Marie and Geelen, Danny and Friml, Jiří and Beeckman, Tom and Vanneste, Steffen}, issn = {1664-462X}, journal = {Frontiers in Plant Science}, publisher = {Frontiers}, title = {{Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana}}, doi = {10.3389/fpls.2022.862398}, volume = {13}, year = {2022}, } @article{11590, abstract = {We investigate the ground-state properties of weakly repulsive one-dimensional bosons in the presence of an attractive zero-range impurity potential. First, we derive mean-field solutions to the problem on a finite ring for the two asymptotic cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering state. Moreover, we derive the critical line that separates these regimes in the parameter space. In the thermodynamic limit, this critical line determines the maximum number of bosons that can be bound by the impurity potential, forming an artificial atom. Second, we validate the mean-field results using the flow equation approach and the multi-layer multi-configuration time-dependent Hartree method for atomic mixtures. While beyond-mean-field effects destroy long-range order in the Bose gas, the critical boson number is unaffected. Our findings are important for understanding such artificial atoms in low-density Bose gases with static and mobile impurities.}, author = {Brauneis, Fabian and Backert, Timothy G. and Mistakidis, Simeon I. and Lemeshko, Mikhail and Hammer, Hans Werner and Volosniev, Artem}, issn = {1367-2630}, journal = {New Journal of Physics}, number = {6}, publisher = {IOP Publishing}, title = {{Artificial atoms from cold bosons in one dimension}}, doi = {10.1088/1367-2630/ac78d8}, volume = {24}, year = {2022}, } @article{11591, abstract = {We investigate the deterministic generation and distribution of entanglement in large quantum networks by driving distant qubits with the output fields of a nondegenerate parametric amplifier. In this setting, the amplifier produces a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated reservoir for the qubits and relaxes them into a highly entangled steady state. Here we are interested in the maximal amount of entanglement and the optimal entanglement generation rates that can be achieved with this scheme under realistic conditions taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation delays into account. By combining exact numerical simulations of the full network with approximate analytic results, we predict the optimal working point for the amplifier and the corresponding qubit-qubit entanglement under various conditions. Our findings show that this passive conversion of Gaussian into discrete-variable entanglement offers a robust and experimentally very attractive approach for operating large optical, microwave, or hybrid quantum networks, for which efficient parametric amplifiers are currently developed.}, author = {Agustí, J. and Minoguchi, Y. and Fink, Johannes M and Rabl, P.}, issn = {2469-9934}, journal = {Physical Review A}, number = {6}, publisher = {American Physical Society}, title = {{Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams}}, doi = {10.1103/PhysRevA.105.062454}, volume = {105}, year = {2022}, }