TY - JOUR
AB - Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.
New method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.
Results: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.
Comparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.
Conclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity.
AU - Zhang, Xiaomin
AU - Schlögl, Alois
AU - Vandael, David H
AU - Jonas, Peter M
ID - 9329
IS - 6
JF - Journal of Neuroscience Methods
SN - 0165-0270
TI - MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo
VL - 357
ER -
TY - JOUR
AB - In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density.
AU - Schöpf, Clemens L.
AU - Ablinger, Cornelia
AU - Geisler, Stefanie M.
AU - Stanika, Ruslan I.
AU - Campiglio, Marta
AU - Kaufmann, Walter
AU - Nimmervoll, Benedikt
AU - Schlick, Bettina
AU - Brockhaus, Johannes
AU - Missler, Markus
AU - Shigemoto, Ryuichi
AU - Obermair, Gerald J.
ID - 9330
IS - 14
JF - PNAS
TI - Presynaptic α2δ subunits are key organizers of glutamatergic synapses
VL - 118
ER -
TY - JOUR
AB - Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale.
AU - Duan, J.
AU - Álvarez-Pérez, G.
AU - Voronin, K. V.
AU - Prieto Gonzalez, Ivan
AU - Taboada-Gutiérrez, J.
AU - Volkov, V. S.
AU - Martín-Sánchez, J.
AU - Nikitin, A. Y.
AU - Alonso-González, P.
ID - 9334
IS - 14
JF - Science Advances
TI - Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition
VL - 7
ER -
TY - JOUR
AB - Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair.
AU - Inglés Prieto, Álvaro
AU - Furthmann, Nikolas
AU - Crossman, Samuel H.
AU - Tichy, Alexandra Madelaine
AU - Hoyer, Nina
AU - Petersen, Meike
AU - Zheden, Vanessa
AU - Bicher, Julia
AU - Gschaider-Reichhart, Eva
AU - György, Attila
AU - Siekhaus, Daria E
AU - Soba, Peter
AU - Winklhofer, Konstanze F.
AU - Janovjak, Harald L
ID - 9363
IS - 4
JF - PLoS genetics
TI - Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease
VL - 17
ER -
TY - JOUR
AB - The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM.
AU - Gast, Matthieu
AU - Kadzioch, Nicole P.
AU - Milius, Doreen
AU - Origgi, Francesco
AU - Plattet, Philippe
ID - 9361
IS - 2
JF - mSphere
TI - Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein
VL - 6
ER -
TY - JOUR
AB - The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.
AU - Prattes, Michael
AU - Grishkovskaya, Irina
AU - Hodirnau, Victor-Valentin
AU - Rössler, Ingrid
AU - Klein, Isabella
AU - Hetzmannseder, Christina
AU - Zisser, Gertrude
AU - Gruber, Christian C.
AU - Gruber, Karl
AU - Haselbach, David
AU - Bergler, Helmut
ID - 9540
IS - 1
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
TI - Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine
VL - 12
ER -
TY - JOUR
AB - While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use.
AU - Bespalov, Anton
AU - Bernard, René
AU - Gilis, Anja
AU - Gerlach, Björn
AU - Guillén, Javier
AU - Castagné, Vincent
AU - Lefevre, Isabel A.
AU - Ducrey, Fiona
AU - Monk, Lee
AU - Bongiovanni, Sandrine
AU - Altevogt, Bruce
AU - Arroyo-Araujo, María
AU - Bikovski, Lior
AU - De Bruin, Natasja
AU - Castaños-Vélez, Esmeralda
AU - Dityatev, Alexander
AU - Emmerich, Christoph H.
AU - Fares, Raafat
AU - Ferland-Beckham, Chantelle
AU - Froger-Colléaux, Christelle
AU - Gailus-Durner, Valerie
AU - Hölter, Sabine M.
AU - Hofmann, Martine Cj
AU - Kabitzke, Patricia
AU - Kas, Martien Jh
AU - Kurreck, Claudia
AU - Moser, Paul
AU - Pietraszek, Malgorzata
AU - Popik, Piotr
AU - Potschka, Heidrun
AU - Prado Montes De Oca, Ernesto
AU - Restivo, Leonardo
AU - Riedel, Gernot
AU - Ritskes-Hoitinga, Merel
AU - Samardzic, Janko
AU - Schunn, Michael
AU - Stöger, Claudia
AU - Voikar, Vootele
AU - Vollert, Jan
AU - Wever, Kimberley E.
AU - Wuyts, Kathleen
AU - Macleod, Malcolm R.
AU - Dirnagl, Ulrich
AU - Steckler, Thomas
ID - 9607
JF - eLife
TI - Introduction to the EQIPD quality system
VL - 10
ER -
TY - JOUR
AB - Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.
AU - Contreras, Ximena
AU - Amberg, Nicole
AU - Davaatseren, Amarbayasgalan
AU - Hansen, Andi H
AU - Sonntag, Johanna
AU - Andersen, Lill
AU - Bernthaler, Tina
AU - Streicher, Carmen
AU - Heger, Anna-Magdalena
AU - Johnson, Randy L.
AU - Schwarz, Lindsay A.
AU - Luo, Liqun
AU - Rülicke, Thomas
AU - Hippenmeyer, Simon
ID - 9603
IS - 12
JF - Cell Reports
TI - A genome-wide library of MADM mice for single-cell genetic mosaic analysis
VL - 35
ER -
TY - JOUR
AB - Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.
AU - Zisis, Themistoklis
AU - Schwarz, Jan
AU - Balles, Miriam
AU - Kretschmer, Maibritt
AU - Nemethova, Maria
AU - Chait, Remy P
AU - Hauschild, Robert
AU - Lange, Janina
AU - Guet, Calin C
AU - Sixt, Michael K
AU - Zahler, Stefan
ID - 9822
IS - 30
JF - ACS Applied Materials and Interfaces
SN - 19448244
TI - Sequential and switchable patterning for studying cellular processes under spatiotemporal control
VL - 13
ER -
TY - JOUR
AB - A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
AU - Nelson, Glyn
AU - Boehm, Ulrike
AU - Bagley, Steve
AU - Bajcsy, Peter
AU - Bischof, Johanna
AU - Brown, Claire M.
AU - Dauphin, Aurélien
AU - Dobbie, Ian M.
AU - Eriksson, John E.
AU - Faklaris, Orestis
AU - Fernandez-Rodriguez, Julia
AU - Ferrand, Alexia
AU - Gelman, Laurent
AU - Gheisari, Ali
AU - Hartmann, Hella
AU - Kukat, Christian
AU - Laude, Alex
AU - Mitkovski, Miso
AU - Munck, Sebastian
AU - North, Alison J.
AU - Rasse, Tobias M.
AU - Resch-Genger, Ute
AU - Schuetz, Lucas C.
AU - Seitz, Arne
AU - Strambio-De-Castillia, Caterina
AU - Swedlow, Jason R.
AU - Alexopoulos, Ioannis
AU - Aumayr, Karin
AU - Avilov, Sergiy
AU - Bakker, Gert Jan
AU - Bammann, Rodrigo R.
AU - Bassi, Andrea
AU - Beckert, Hannes
AU - Beer, Sebastian
AU - Belyaev, Yury
AU - Bierwagen, Jakob
AU - Birngruber, Konstantin A.
AU - Bosch, Manel
AU - Breitlow, Juergen
AU - Cameron, Lisa A.
AU - Chalfoun, Joe
AU - Chambers, James J.
AU - Chen, Chieh Li
AU - Conde-Sousa, Eduardo
AU - Corbett, Alexander D.
AU - Cordelieres, Fabrice P.
AU - Nery, Elaine Del
AU - Dietzel, Ralf
AU - Eismann, Frank
AU - Fazeli, Elnaz
AU - Felscher, Andreas
AU - Fried, Hans
AU - Gaudreault, Nathalie
AU - Goh, Wah Ing
AU - Guilbert, Thomas
AU - Hadleigh, Roland
AU - Hemmerich, Peter
AU - Holst, Gerhard A.
AU - Itano, Michelle S.
AU - Jaffe, Claudia B.
AU - Jambor, Helena K.
AU - Jarvis, Stuart C.
AU - Keppler, Antje
AU - Kirchenbuechler, David
AU - Kirchner, Marcel
AU - Kobayashi, Norio
AU - Krens, Gabriel
AU - Kunis, Susanne
AU - Lacoste, Judith
AU - Marcello, Marco
AU - Martins, Gabriel G.
AU - Metcalf, Daniel J.
AU - Mitchell, Claire A.
AU - Moore, Joshua
AU - Mueller, Tobias
AU - Nelson, Michael S.
AU - Ogg, Stephen
AU - Onami, Shuichi
AU - Palmer, Alexandra L.
AU - Paul-Gilloteaux, Perrine
AU - Pimentel, Jaime A.
AU - Plantard, Laure
AU - Podder, Santosh
AU - Rexhepaj, Elton
AU - Royon, Arnaud
AU - Saari, Markku A.
AU - Schapman, Damien
AU - Schoonderwoert, Vincent
AU - Schroth-Diez, Britta
AU - Schwartz, Stanley
AU - Shaw, Michael
AU - Spitaler, Martin
AU - Stoeckl, Martin T.
AU - Sudar, Damir
AU - Teillon, Jeremie
AU - Terjung, Stefan
AU - Thuenauer, Roland
AU - Wilms, Christian D.
AU - Wright, Graham D.
AU - Nitschke, Roland
ID - 9911
IS - 1
JF - Journal of Microscopy
SN - 0022-2720
TI - QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
VL - 284
ER -
TY - JOUR
AB - Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials.
AU - Liu, Yu
AU - Calcabrini, Mariano
AU - Yu, Yuan
AU - Genç, Aziz
AU - Chang, Cheng
AU - Costanzo, Tommaso
AU - Kleinhanns, Tobias
AU - Lee, Seungho
AU - Llorca, Jordi
AU - Cojocaru‐Mirédin, Oana
AU - Ibáñez, Maria
ID - 10123
IS - 52
JF - Advanced Materials
KW - mechanical engineering
KW - mechanics of materials
KW - general materials science
SN - 0935-9648
TI - The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe
VL - 33
ER -
TY - JOUR
AB - Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.
AU - Artan, Murat
AU - Barratt, Stephen
AU - Flynn, Sean M.
AU - Begum, Farida
AU - Skehel, Mark
AU - Nicolas, Armel
AU - De Bono, Mario
ID - 10117
IS - 3
JF - Journal of Biological Chemistry
SN - 0021-9258
TI - Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling
VL - 297
ER -
TY - JOUR
AB - Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials.
AU - Martín-Sánchez, Javier
AU - Duan, Jiahua
AU - Taboada-Gutiérrez, Javier
AU - Álvarez-Pérez, Gonzalo
AU - Voronin, Kirill V.
AU - Prieto Gonzalez, Ivan
AU - Ma, Weiliang
AU - Bao, Qiaoliang
AU - Volkov, Valentyn S.
AU - Hillenbrand, Rainer
AU - Nikitin, Alexey Y.
AU - Alonso-González, Pablo
ID - 10177
IS - 41
JF - Science Advances
TI - Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas
VL - 7
ER -
TY - JOUR
AB - Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling.
AU - Bajaj, Sunanjay
AU - Bagley, Joshua A.
AU - Sommer, Christoph M
AU - Vertesy, Abel
AU - Nagumo Wong, Sakurako
AU - Krenn, Veronica
AU - Lévi-Strauss, Julie
AU - Knoblich, Juergen A.
ID - 10179
IS - 23
JF - EMBO Journal
SN - 0261-4189
TI - Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration
VL - 40
ER -
TY - JOUR
AB - During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.
AU - Restivo, Leonardo
AU - Gerlach, Björn
AU - Tsoory, Michael
AU - Bikovski, Lior
AU - Badurek, Sylvia
AU - Pitzer, Claudia
AU - Kos-Braun, Isabelle C.
AU - Mausset-Bonnefont, Anne Laure Mj
AU - Ward, Jonathan
AU - Schunn, Michael
AU - Noldus, Lucas P.J.J.
AU - Bespalov, Anton
AU - Voikar, Vootele
ID - 10283
JF - EMBO Reports
SN - 1469-221X
TI - Towards best practices in research: Role of academic core facilities
VL - 22
ER -
TY - JOUR
AB - The evidence linking innate immunity mechanisms and neurodegenerative diseases is growing, but the specific mechanisms are incompletely understood. Experimental data suggest that microglial TLR4 mediates the uptake and clearance of α-synuclein also termed synucleinophagy. The accumulation of misfolded α-synuclein throughout the brain is central to Parkinson's disease (PD). The distribution and progression of the pathology is often attributed to the propagation of α-synuclein. Here, we apply a classical α-synuclein propagation model of prodromal PD in wild type and TLR4 deficient mice to study the role of TLR4 in the progression of the disease. Our data suggest that TLR4 deficiency facilitates the α-synuclein seed spreading associated with reduced lysosomal activity of microglia. Three months after seed inoculation, more pronounced proteinase K-resistant α-synuclein inclusion pathology is observed in mice with TLR4 deficiency. The facilitated propagation of α-synuclein is associated with early loss of dopamine transporter (DAT) signal in the striatum and loss of dopaminergic neurons in substantia nigra pars compacta of TLR4 deficient mice. These new results support TLR4 signaling as a putative target for disease modification to slow the progression of PD and related disorders.
AU - Venezia, Serena
AU - Kaufmann, Walter
AU - Wenning, Gregor K.
AU - Stefanova, Nadia
ID - 10607
JF - Parkinsonism & Related Disorders
SN - 1353-8020
TI - Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease
VL - 91
ER -
TY - JOUR
AB - Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.
AU - Prehal, Christian
AU - Samojlov, Aleksej
AU - Nachtnebel, Manfred
AU - Lovicar, Ludek
AU - Kriechbaum, Manfred
AU - Amenitsch, Heinz
AU - Freunberger, Stefan Alexander
ID - 9301
IS - 14
JF - Proceedings of the National Academy of Sciences
KW - small-angle X-ray scattering
KW - oxygen reduction
KW - disproportionation
KW - Li-air battery
SN - 0027-8424
TI - In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes
VL - 118
ER -
TY - JOUR
AU - Pranger, Christina L.
AU - Fazekas-Singer, Judit
AU - Köhler, Verena K.
AU - Pali‐Schöll, Isabella
AU - Fiocchi, Alessandro
AU - Karagiannis, Sophia N.
AU - Zenarruzabeitia, Olatz
AU - Borrego, Francisco
AU - Jensen‐Jarolim, Erika
ID - 10836
IS - 5
JF - Allergy
KW - Immunology
KW - Immunology and Allergy
SN - 0105-4538
TI - PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance
VL - 76
ER -
TY - JOUR
AB - There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits.
AU - Peruzzo, Matilda
AU - Hassani, Farid
AU - Szep, Gregory
AU - Trioni, Andrea
AU - Redchenko, Elena
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 9928
IS - 4
JF - PRX Quantum
KW - quantum physics
KW - mesoscale and nanoscale physics
TI - Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction
VL - 2
ER -
TY - JOUR
AB - Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.
AU - Li, Lanxin
AU - Verstraeten, Inge
AU - Roosjen, Mark
AU - Takahashi, Koji
AU - Rodriguez Solovey, Lesia
AU - Merrin, Jack
AU - Chen, Jian
AU - Shabala, Lana
AU - Smet, Wouter
AU - Ren, Hong
AU - Vanneste, Steffen
AU - Shabala, Sergey
AU - De Rybel, Bert
AU - Weijers, Dolf
AU - Kinoshita, Toshinori
AU - Gray, William M.
AU - Friml, Jiří
ID - 10223
IS - 7884
JF - Nature
KW - Multidisciplinary
SN - 00280836
TI - Cell surface and intracellular auxin signalling for H+ fluxes in root growth
VL - 599
ER -
TY - JOUR
AB - Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.
AU - Johnson, Alexander J
AU - Dahhan, Dana A
AU - Gnyliukh, Nataliia
AU - Kaufmann, Walter
AU - Zheden, Vanessa
AU - Costanzo, Tommaso
AU - Mahou, Pierre
AU - Hrtyan, Mónika
AU - Wang, Jie
AU - Aguilera Servin, Juan L
AU - van Damme, Daniël
AU - Beaurepaire, Emmanuel
AU - Loose, Martin
AU - Bednarek, Sebastian Y
AU - Friml, Jiří
ID - 9887
IS - 51
JF - Proceedings of the National Academy of Sciences
TI - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis
VL - 118
ER -
TY - JOUR
AB - A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.
AU - Valentini, Marco
AU - Peñaranda, Fernando
AU - Hofmann, Andrea C
AU - Brauns, Matthias
AU - Hauschild, Robert
AU - Krogstrup, Peter
AU - San-Jose, Pablo
AU - Prada, Elsa
AU - Aguado, Ramón
AU - Katsaros, Georgios
ID - 8910
IS - 6550
JF - Science
SN - 00368075
TI - Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states
VL - 373
ER -
TY - COMP
AB - Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.
AU - Guzmán, José
AU - Schlögl, Alois
AU - Espinoza Martinez, Claudia
AU - Zhang, Xiaomin
AU - Suter, Benjamin
AU - Jonas, Peter M
ID - 10110
TI - How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network
ER -
TY - JOUR
AB - De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.
AU - Morandell, Jasmin
AU - Schwarz, Lena A
AU - Basilico, Bernadette
AU - Tasciyan, Saren
AU - Dimchev, Georgi A
AU - Nicolas, Armel
AU - Sommer, Christoph M
AU - Kreuzinger, Caroline
AU - Dotter, Christoph
AU - Knaus, Lisa
AU - Dobler, Zoe
AU - Cacci, Emanuele
AU - Schur, Florian KM
AU - Danzl, Johann G
AU - Novarino, Gaia
ID - 9429
IS - 1
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
TI - Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development
VL - 12
ER -
TY - JOUR
AB - Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.
AU - Jirovec, Daniel
AU - Hofmann, Andrea C
AU - Ballabio, Andrea
AU - Mutter, Philipp M.
AU - Tavani, Giulio
AU - Botifoll, Marc
AU - Crippa, Alessandro
AU - Kukucka, Josip
AU - Sagi, Oliver
AU - Martins, Frederico
AU - Saez Mollejo, Jaime
AU - Prieto Gonzalez, Ivan
AU - Borovkov, Maksim
AU - Arbiol, Jordi
AU - Chrastina, Daniel
AU - Isella, Giovanni
AU - Katsaros, Georgios
ID - 8909
IS - 8
JF - Nature Materials
SN - 1476-1122
TI - A singlet triplet hole spin qubit in planar Ge
VL - 20
ER -
TY - CHAP
AB - High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.
AU - Kaufmann, Walter
AU - Kleindienst, David
AU - Harada, Harumi
AU - Shigemoto, Ryuichi
ID - 9756
KW - Freeze-fracture replica: Deep learning
KW - Immunogold labeling
KW - Integral membrane protein
KW - Electron microscopy
SN - 9781071615218
T2 - Receptor and Ion Channel Detection in the Brain
TI - High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)
VL - 169
ER -
TY - JOUR
AB - Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.
Here we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.
The gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.
AU - Gelová, Zuzana
AU - Gallei, Michelle C
AU - Pernisová, Markéta
AU - Brunoud, Géraldine
AU - Zhang, Xixi
AU - Glanc, Matous
AU - Li, Lanxin
AU - Michalko, Jaroslav
AU - Pavlovicova, Zlata
AU - Verstraeten, Inge
AU - Han, Huibin
AU - Hajny, Jakub
AU - Hauschild, Robert
AU - Čovanová, Milada
AU - Zwiewka, Marta
AU - Hörmayer, Lukas
AU - Fendrych, Matyas
AU - Xu, Tongda
AU - Vernoux, Teva
AU - Friml, Jiří
ID - 8931
JF - Plant Science
KW - Agronomy and Crop Science
KW - Plant Science
KW - Genetics
KW - General Medicine
SN - 0168-9452
TI - Developmental roles of auxin binding protein 1 in Arabidopsis thaliana
VL - 303
ER -
TY - GEN
AB - Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.
AU - Li, Lanxin
AU - Verstraeten, Inge
AU - Roosjen, Mark
AU - Takahashi, Koji
AU - Rodriguez Solovey, Lesia
AU - Merrin, Jack
AU - Chen, Jian
AU - Shabala, Lana
AU - Smet, Wouter
AU - Ren, Hong
AU - Vanneste, Steffen
AU - Shabala, Sergey
AU - De Rybel, Bert
AU - Weijers, Dolf
AU - Kinoshita, Toshinori
AU - Gray, William M.
AU - Friml, Jiří
ID - 10095
SN - 2693-5015
T2 - Research Square
TI - Cell surface and intracellular auxin signalling for H+-fluxes in root growth
ER -
TY - COMP
AU - Hauschild, Robert
ID - 8181
TI - Amplified centrosomes in dendritic cells promote immune cell effector functions
ER -
TY - COMP
AB - Automated root growth analysis and tracking of root tips.
AU - Hauschild, Robert
ID - 8294
TI - RGtracker
ER -
TY - GEN
AB - A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group "Open Science Strategy" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions.
AU - Mayer, Katja
AU - Rieck, Katharina
AU - Reichmann, Stefan
AU - Danowski, Patrick
AU - Graschopf, Anton
AU - König, Thomas
AU - Kraker, Peter
AU - Lehner, Patrick
AU - Reckling, Falk
AU - Ross-Hellauer, Tony
AU - Spichtinger, Daniel
AU - Tzatzanis, Michalis
AU - Schürz, Stefanie
ID - 8695
TI - Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria
ER -
TY - JOUR
AB - As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level.
AU - Danowski, Patrick
AU - Ferus, Andreas
AU - Hikl, Anna-Laetitia
AU - McNeill, Gerda
AU - Miniberger, Clemens
AU - Reding, Steve
AU - Zarka, Tobias
AU - Zojer, Michael
ID - 8706
IS - 2
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
TI - „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B
VL - 73
ER -
TY - BOOK
AB - This booklet is a collection of abstracts presented at the AHPC conference.
ED - Schlögl, Alois
ED - Kiss, Janos
ED - Elefante, Stefano
ID - 7474
SN - 978-3-99078-004-6
TI - Austrian High-Performance-Computing meeting (AHPC2020)
ER -
TY - JOUR
AB - In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.
AU - Narasimhan, Madhumitha
AU - Johnson, Alexander J
AU - Prizak, Roshan
AU - Kaufmann, Walter
AU - Tan, Shutang
AU - Casillas Perez, Barbara E
AU - Friml, Jiří
ID - 7490
JF - eLife
TI - Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants
VL - 9
ER -
TY - JOUR
AB - Phonon polaritons—light coupled to lattice vibrations—in polar van der Waals crystals are promising candidates for controlling the flow of energy on the nanoscale due to their strong field confinement, anisotropic propagation and ultra-long lifetime in the picosecond range1,2,3,4,5. However, the lack of tunability of their narrow and material-specific spectral range—the Reststrahlen band—severely limits their technological implementation. Here, we demonstrate that intercalation of Na atoms in the van der Waals semiconductor α-V2O5 enables a broad spectral shift of Reststrahlen bands, and that the phonon polaritons excited show ultra-low losses (lifetime of 4 ± 1 ps), similar to phonon polaritons in a non-intercalated crystal (lifetime of 6 ± 1 ps). We expect our intercalation method to be applicable to other van der Waals crystals, opening the door for the use of phonon polaritons in broad spectral bands in the mid-infrared domain.
AU - Taboada-Gutiérrez, Javier
AU - Álvarez-Pérez, Gonzalo
AU - Duan, Jiahua
AU - Ma, Weiliang
AU - Crowley, Kyle
AU - Prieto Gonzalez, Ivan
AU - Bylinkin, Andrei
AU - Autore, Marta
AU - Volkova, Halyna
AU - Kimura, Kenta
AU - Kimura, Tsuyoshi
AU - Berger, M. H.
AU - Li, Shaojuan
AU - Bao, Qiaoliang
AU - Gao, Xuan P.A.
AU - Errea, Ion
AU - Nikitin, Alexey Y.
AU - Hillenbrand, Rainer
AU - Martín-Sánchez, Javier
AU - Alonso-González, Pablo
ID - 7792
JF - Nature Materials
SN - 14761122
TI - Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation
VL - 19
ER -
TY - JOUR
AB - Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.
AU - Kopf, Aglaja
AU - Renkawitz, Jörg
AU - Hauschild, Robert
AU - Girkontaite, Irute
AU - Tedford, Kerry
AU - Merrin, Jack
AU - Thorn-Seshold, Oliver
AU - Trauner, Dirk
AU - Häcker, Hans
AU - Fischer, Klaus Dieter
AU - Kiermaier, Eva
AU - Sixt, Michael K
ID - 7875
IS - 6
JF - The Journal of Cell Biology
TI - Microtubules control cellular shape and coherence in amoeboid migrating cells
VL - 219
ER -
TY - JOUR
AB - Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.
AU - Schauer, Alexandra
AU - Nunes Pinheiro, Diana C
AU - Hauschild, Robert
AU - Heisenberg, Carl-Philipp J
ID - 7888
JF - eLife
SN - 2050-084X
TI - Zebrafish embryonic explants undergo genetically encoded self-assembly
VL - 9
ER -
TY - JOUR
AB - Purpose of review: Cancer is one of the leading causes of death and the incidence rates are constantly rising. The heterogeneity of tumors poses a big challenge for the treatment of the disease and natural antibodies additionally affect disease progression. The introduction of engineered mAbs for anticancer immunotherapies has substantially improved progression-free and overall survival of cancer patients, but little efforts have been made to exploit other antibody isotypes than IgG.
Recent findings: In order to improve these therapies, ‘next-generation antibodies’ were engineered to enhance a specific feature of classical antibodies and form a group of highly effective and precise therapy compounds. Advanced antibody approaches include among others antibody-drug conjugates, glyco-engineered and Fc-engineered antibodies, antibody fragments, radioimmunotherapy compounds, bispecific antibodies and alternative (non-IgG) immunoglobulin classes, especially IgE.
Summary: The current review describes solutions for the needs of next-generation antibody therapies through different approaches. Careful selection of the best-suited engineering methodology is a key factor in developing personalized, more specific and more efficient mAbs against cancer to improve the outcomes of cancer patients. We highlight here the large evidence of IgE exploiting a highly cytotoxic effector arm as potential next-generation anticancer immunotherapy.
AU - Singer, Judit
AU - Singer, Josef
AU - Jensen-Jarolim, Erika
ID - 7864
IS - 3
JF - Current opinion in allergy and clinical immunology
TI - Precision medicine in clinical oncology: the journey from IgG antibody to IgE
VL - 20
ER -
TY - JOUR
AB - Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.
AU - Zhang, Xiaomin
AU - Schlögl, Alois
AU - Jonas, Peter M
ID - 8261
IS - 6
JF - Neuron
SN - 0896-6273
TI - Selective routing of spatial information flow from input to output in hippocampal granule cells
VL - 107
ER -
TY - JOUR
AB - Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.
AU - Merrin, Jack
ID - 8597
IS - 6
JF - Physical Biology
TI - Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide
VL - 17
ER -
TY - JOUR
AB - Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
AU - Schulte, Linda
AU - Mao, Jiafei
AU - Reitz, Julian
AU - Sreeramulu, Sridhar
AU - Kudlinzki, Denis
AU - Hodirnau, Victor-Valentin
AU - Meier-Credo, Jakob
AU - Saxena, Krishna
AU - Buhr, Florian
AU - Langer, Julian D.
AU - Blackledge, Martin
AU - Frangakis, Achilleas S.
AU - Glaubitz, Clemens
AU - Schwalbe, Harald
ID - 8744
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cysteine oxidation and disulfide formation in the ribosomal exit tunnel
VL - 11
ER -
TY - JOUR
AB - Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets.
AU - Nicolai, Leo
AU - Schiefelbein, Karin
AU - Lipsky, Silvia
AU - Leunig, Alexander
AU - Hoffknecht, Marie
AU - Pekayvaz, Kami
AU - Raude, Ben
AU - Marx, Charlotte
AU - Ehrlich, Andreas
AU - Pircher, Joachim
AU - Zhang, Zhe
AU - Saleh, Inas
AU - Marel, Anna-Kristina
AU - Löf, Achim
AU - Petzold, Tobias
AU - Lorenz, Michael
AU - Stark, Konstantin
AU - Pick, Robert
AU - Rosenberger, Gerhild
AU - Weckbach, Ludwig
AU - Uhl, Bernd
AU - Xia, Sheng
AU - Reichel, Christoph Andreas
AU - Walzog, Barbara
AU - Schulz, Christian
AU - Zheden, Vanessa
AU - Bender, Markus
AU - Li, Rong
AU - Massberg, Steffen
AU - Gärtner, Florian R
ID - 8787
JF - Nature Communications
TI - Vascular surveillance by haptotactic blood platelets in inflammation and infection
VL - 11
ER -
TY - JOUR
AB - The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.
AU - Fäßler, Florian
AU - Dimchev, Georgi A
AU - Hodirnau, Victor-Valentin
AU - Wan, William
AU - Schur, Florian KM
ID - 8971
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction
VL - 11
ER -
TY - JOUR
AB - Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management.
AU - Duan, Jiahua
AU - Capote-Robayna, Nathaniel
AU - Taboada-Gutiérrez, Javier
AU - Álvarez-Pérez, Gonzalo
AU - Prieto Gonzalez, Ivan
AU - Martín-Sánchez, Javier
AU - Nikitin, Alexey Y.
AU - Alonso-González, Pablo
ID - 10866
IS - 7
JF - Nano Letters
KW - Mechanical Engineering
KW - Condensed Matter Physics
KW - General Materials Science
KW - General Chemistry
KW - Bioengineering
SN - 1530-6984
TI - Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs
VL - 20
ER -
TY - JOUR
AB - A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.
AU - Ernst, Doris
AU - Novotny, Gertraud
AU - Schönher, Eva Maria
ID - 7687
IS - 1
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
SN - 1022-2588
TI - (Core Trust) Seal your repository!
VL - 73
ER -
TY - GEN
AB - De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages.
AU - Morandell, Jasmin
AU - Schwarz, Lena A
AU - Basilico, Bernadette
AU - Tasciyan, Saren
AU - Nicolas, Armel
AU - Sommer, Christoph M
AU - Kreuzinger, Caroline
AU - Knaus, Lisa
AU - Dobler, Zoe
AU - Cacci, Emanuele
AU - Danzl, Johann G
AU - Novarino, Gaia
ID - 7800
T2 - bioRxiv
TI - Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development
ER -
TY - GEN
AB - Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.
AU - Slovakova, Jana
AU - Sikora, Mateusz K
AU - Caballero Mancebo, Silvia
AU - Krens, Gabriel
AU - Kaufmann, Walter
AU - Huljev, Karla
AU - Heisenberg, Carl-Philipp J
ID - 9750
T2 - bioRxiv
TI - Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
ER -
TY - JOUR
AB - Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.
AU - Reversat, Anne
AU - Gärtner, Florian R
AU - Merrin, Jack
AU - Stopp, Julian A
AU - Tasciyan, Saren
AU - Aguilera Servin, Juan L
AU - De Vries, Ingrid
AU - Hauschild, Robert
AU - Hons, Miroslav
AU - Piel, Matthieu
AU - Callan-Jones, Andrew
AU - Voituriez, Raphael
AU - Sixt, Michael K
ID - 7885
JF - Nature
SN - 00280836
TI - Cellular locomotion using environmental topography
VL - 582
ER -
TY - JOUR
AB - Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.
AU - Johnson, Alexander J
AU - Gnyliukh, Nataliia
AU - Kaufmann, Walter
AU - Narasimhan, Madhumitha
AU - Vert, G
AU - Bednarek, SY
AU - Friml, Jiří
ID - 8139
IS - 15
JF - Journal of Cell Science
SN - 0021-9533
TI - Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis
VL - 133
ER -
TY - JOUR
AB - Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.
AU - Antoniou, Michael N.
AU - Nicolas, Armel
AU - Mesnage, Robin
AU - Biserni, Martina
AU - Rao, Francesco V.
AU - Martin, Cristina Vazquez
ID - 6819
JF - BMC Research Notes
TI - Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells
VL - 12
ER -
TY - GEN
AB - Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.
AU - Antoniou, Michael N.
AU - Nicolas, Armel
AU - Mesnage, Robin
AU - Biserni, Martina
AU - Rao, Francesco V.
AU - Martin, Cristina Vazquez
ID - 9784
TI - MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells
ER -
TY - GEN
AU - Schlögl, Alois
AU - Kiss, Janos
AU - Elefante, Stefano
ID - 12901
T2 - AHPC19 - Austrian HPC Meeting 2019
TI - Is Debian suitable for running an HPC Cluster?
ER -
TY - JOUR
AB - Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.
AU - Truckenbrodt, Sven M
AU - Sommer, Christoph M
AU - Rizzoli, Silvio O
AU - Danzl, Johann G
ID - 6052
IS - 3
JF - Nature Protocols
TI - A practical guide to optimization in X10 expansion microscopy
VL - 14
ER -
TY - JOUR
AB - Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity.
AU - Xia, Peng
AU - Gütl, Daniel J
AU - Zheden, Vanessa
AU - Heisenberg, Carl-Philipp J
ID - 6087
IS - 6
JF - Cell
TI - Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity
VL - 176
ER -
TY - JOUR
AB - Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically.
AU - Nguyen, Chi Huu
AU - Glüxam, Tobias
AU - Schlerka, Angela
AU - Bauer, Katharina
AU - Grandits, Alexander M.
AU - Hackl, Hubert
AU - Dovey, Oliver
AU - Zöchbauer-Müller, Sabine
AU - Cooper, Jonathan L.
AU - Vassiliou, George S.
AU - Stoiber, Dagmar
AU - Wieser, Rotraud
AU - Heller, Gerwin
ID - 6607
IS - 1
JF - Scientific Reports
TI - SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness
VL - 9
ER -
TY - JOUR
AB - A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories.
AU - Fenu, M.
AU - Bettermann, T.
AU - Vogl, C.
AU - Darwish-Miranda, Nasser
AU - Schramel, J.
AU - Jenner, F.
AU - Ribitsch, I.
ID - 6867
IS - 1
JF - Scientific Reports
TI - A novel magnet-based scratch method for standardisation of wound-healing assays
VL - 9
ER -
TY - JOUR
AB - This is a literature teaching resource review for biologically inspired microfluidics courses
or exploring the diverse applications of microfluidics. The structure is around key papers and model
organisms. While courses gradually change over time, a focus remains on understanding how
microfluidics has developed as well as what it can and cannot do for researchers. As a primary
starting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety
of applications are discussed using model prokaryotic and eukaryotic organisms from the set
of bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),
slime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),
plants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and
biochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,
biotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,
microfluidics can still be used effectively for specific applications.
AU - Merrin, Jack
ID - 7225
IS - 4
JF - Bioengineering
TI - Frontiers in microfluidics, a teaching resource review
VL - 6
ER -
TY - JOUR
AB - Background
Synaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.
New method
Here, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.
Results
We show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.
Comparison with existing methods
Obtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.
Conclusions
These results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.
AU - Mckenzie, Catherine
AU - Spanova, Miroslava
AU - Johnson, Alexander J
AU - Kainrath, Stephanie
AU - Zheden, Vanessa
AU - Sitte, Harald H.
AU - Janovjak, Harald L
ID - 7406
JF - Journal of Neuroscience Methods
SN - 0165-0270
TI - Isolation of synaptic vesicles from genetically engineered cultured neurons
VL - 312
ER -
TY - JOUR
AU - Morandell, Jasmin
AU - Nicolas, Armel
AU - Schwarz, Lena A
AU - Novarino, Gaia
ID - 7415
IS - Supplement 6
JF - European Neuropsychopharmacology
SN - 0924-977X
TI - S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism
VL - 29
ER -
TY - JOUR
AB - Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source.
AU - Goudarzi, Mohammad
AU - Boquet-Pujadas, Aleix
AU - Olivo-Marin, Jean Christophe
AU - Raz, Erez
ID - 6093
IS - 2
JF - PLOS ONE
TI - Fluid dynamics during bleb formation in migrating cells in vivo
VL - 14
ER -
TY - JOUR
AB - In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as "gold" and "green" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.
AU - Danowski, Patrick
ID - 6657
IS - 1
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
TI - An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors
VL - 72
ER -
TY - JOUR
AB - During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.
AU - Renkawitz, Jörg
AU - Kopf, Aglaja
AU - Stopp, Julian A
AU - de Vries, Ingrid
AU - Driscoll, Meghan K.
AU - Merrin, Jack
AU - Hauschild, Robert
AU - Welf, Erik S.
AU - Danuser, Gaudenz
AU - Fiolka, Reto
AU - Sixt, Michael K
ID - 6328
JF - Nature
TI - Nuclear positioning facilitates amoeboid migration along the path of least resistance
VL - 568
ER -
TY - JOUR
AB - In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation.
AU - Petritsch, Barbara
AU - Porsche, Jana
ID - 53
IS - 1
JF - VÖB Mitteilungen
TI - IST PubRep and IST DataRep: the institutional repositories at IST Austria
VL - 71
ER -
TY - GEN
AU - Petritsch, Barbara
ID - 6459
KW - Open Access
KW - Publication Analysis
TI - Open Access at IST Austria 2009-2017
ER -
TY - JOUR
AB - Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo.
AU - Ratheesh, Aparna
AU - Biebl, Julia
AU - Smutny, Michael
AU - Veselá, Jana
AU - Papusheva, Ekaterina
AU - Krens, Gabriel
AU - Kaufmann, Walter
AU - György, Attila
AU - Casano, Alessandra M
AU - Siekhaus, Daria E
ID - 308
IS - 3
JF - Developmental Cell
TI - Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration
VL - 45
ER -
TY - JOUR
AB - Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.
AU - Leithner, Alexander F
AU - Renkawitz, Jörg
AU - De Vries, Ingrid
AU - Hauschild, Robert
AU - Haecker, Hans
AU - Sixt, Michael K
ID - 437
IS - 6
JF - European Journal of Immunology
TI - Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration
VL - 48
ER -
TY - JOUR
AB - Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.
AU - Brown, Markus
AU - Johnson, Louise
AU - Leone, Dario
AU - Májek, Peter
AU - Vaahtomeri, Kari
AU - Senfter, Daniel
AU - Bukosza, Nora
AU - Schachner, Helga
AU - Asfour, Gabriele
AU - Langer, Brigitte
AU - Hauschild, Robert
AU - Parapatics, Katja
AU - Hong, Young
AU - Bennett, Keiryn
AU - Kain, Renate
AU - Detmar, Michael
AU - Sixt, Michael K
AU - Jackson, David
AU - Kerjaschki, Dontscho
ID - 275
IS - 6
JF - Journal of Cell Biology
TI - Lymphatic exosomes promote dendritic cell migration along guidance cues
VL - 217
ER -
TY - CHAP
AB - Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters.
AU - Renkawitz, Jörg
AU - Reversat, Anne
AU - Leithner, Alexander F
AU - Merrin, Jack
AU - Sixt, Michael K
ID - 153
SN - 0091679X
T2 - Methods in Cell Biology
TI - Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments
VL - 147
ER -
TY - JOUR
AB - The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.
AU - Fendrych, Matyas
AU - Akhmanova, Maria
AU - Merrin, Jack
AU - Glanc, Matous
AU - Hagihara, Shinya
AU - Takahashi, Koji
AU - Uchida, Naoyuki
AU - Torii, Keiko U
AU - Friml, Jirí
ID - 192
IS - 7
JF - Nature Plants
TI - Rapid and reversible root growth inhibition by TIR1 auxin signalling
VL - 4
ER -
TY - JOUR
AB - For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.
AU - Reipert, Siegfried
AU - Goldammer, Helmuth
AU - Richardson, Christine
AU - Goldberg, Martin
AU - Hawkins, Timothy
AU - Hollergschwandtner, Elena
AU - Kaufmann, Walter
AU - Antreich, Sebastian
AU - Stierhof, York
ID - 163
IS - 12
JF - Journal of Histochemistry and Cytochemistry
SN - 0022-1554
TI - Agitation modules: Flexible means to accelerate automated freeze substitution
VL - 66
ER -
TY - GEN
AU - Danowski, Patrick
ID - 5686
TI - An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors
ER -
TY - DATA
AB - Data on Austrian open access publication output at Emerald from 2013-2017 including data analysis.
AU - Villányi, Márton
ID - 5577
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Emerald Austrian Publications 2013-2017
ER -
TY - DATA
AB - Data on Austrian open access publication output at IOP from 2012-2015 including data analysis.
AU - Villányi, Márton
ID - 5578
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - IOP Austrian Publications 2012-2015
ER -
TY - DATA
AB - Comparison of Scopus' and publisher's data on Austrian publication output at IOP.
AU - Villányi, Márton
ID - 5574
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Data Check IOP Scopus vs. Publisher
ER -
TY - THES
AB - Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance.
AU - Villányi, Márton
ID - 278
TI - Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken
ER -
TY - DATA
AB - Script to perform a simple exponential lifetime fit of a ROI on time stacks acquired with a FLIM X16 TCSPC detector (+example data)
AU - Hauschild, Robert
ID - 5588
KW - FLIM
KW - FRET
KW - fluorescence lifetime imaging
TI - Fluorescence lifetime analysis of FLIM X16 TCSPC data
ER -
TY - DATA
AB - Data on Austrian open access publication output at Taylor&Francis from 2013-2017 including data analysis.
AU - Villányi, Márton
ID - 5582
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Taylor&Francis Austrian Publications 2013-2017
ER -
TY - DATA
AB - Data on Austrian open access publication output at Springer from 2013-2016 including data analysis.
AU - Villányi, Márton
ID - 5581
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Springer Austrian Publications 2013-2016
ER -
TY - DATA
AB - Data on Austrian open access publication output at SAGE from 2013-2017 including data analysis.
AU - Villányi, Márton
ID - 5580
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - SAGE Austrian Publications 2013-2017
ER -
TY - DATA
AB - Data on Austrian open access publication output at RSC from 2013-2017 including data analysis.
AU - Villányi, Márton
ID - 5579
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - RSC Austrian Publications 2013-2017
ER -
TY - DATA
AB - Comparison of Scopus' and FWF's data on Austrian publication output at T&F.
AU - Villányi, Márton
ID - 5576
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Data Check T&F Scopus vs. FWF
ER -
TY - DATA
AB - Comparison of Scopus' and FWF's data on Austrian publication output at RSC.
AU - Villányi, Márton
ID - 5575
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Data Check RSC Scopus vs. FWF
ER -
TY - JOUR
AB - Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux.
AU - Hons, Miroslav
AU - Kopf, Aglaja
AU - Hauschild, Robert
AU - Leithner, Alexander F
AU - Gärtner, Florian R
AU - Abe, Jun
AU - Renkawitz, Jörg
AU - Stein, Jens
AU - Sixt, Michael K
ID - 15
IS - 6
JF - Nature Immunology
TI - Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells
VL - 19
ER -
TY - JOUR
AB - The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH.
AU - Li, Lanxin
AU - Krens, Gabriel
AU - Fendrych, Matyas
AU - Friml, Jirí
ID - 442
IS - 1
JF - Bio-protocol
TI - Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls
VL - 8
ER -
TY - GEN
AB - In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.
AU - Barbara Petritsch
ID - 5450
TI - Implementing the institutional data repository IST DataRep
ER -
TY - CONF
AB - Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.
AU - Sauermann, Stefan
AU - David, Veronika
AU - Schlögl, Alois
AU - Egelkraut, Reinhard
AU - Frohner, Matthias
AU - Pohn, Birgit
AU - Urbauer, Philipp
AU - Mense, Alexander
ID - 630
SN - 978-161499758-0
TI - Biosignals standards and FHIR: The way to go
VL - 236
ER -
TY - JOUR
AB - Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.
AU - Vaahtomeri, Kari
AU - Brown, Markus
AU - Hauschild, Robert
AU - De Vries, Ingrid
AU - Leithner, Alexander F
AU - Mehling, Matthias
AU - Kaufmann, Walter
AU - Sixt, Michael K
ID - 672
IS - 5
JF - Cell Reports
SN - 22111247
TI - Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia
VL - 19
ER -
TY - JOUR
AB - Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.
AU - Schwarz, Jan
AU - Bierbaum, Veronika
AU - Vaahtomeri, Kari
AU - Hauschild, Robert
AU - Brown, Markus
AU - De Vries, Ingrid
AU - Leithner, Alexander F
AU - Reversat, Anne
AU - Merrin, Jack
AU - Tarrant, Teresa
AU - Bollenbach, Tobias
AU - Sixt, Michael K
ID - 674
IS - 9
JF - Current Biology
SN - 09609822
TI - Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6
VL - 27
ER -
TY - JOUR
AB - Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels.
AU - Miki, Takafumi
AU - Kaufmann, Walter
AU - Malagon, Gerardo
AU - Gomez, Laura
AU - Tabuchi, Katsuhiko
AU - Watanabe, Masahiko
AU - Shigemoto, Ryuichi
AU - Marty, Alain
ID - 693
IS - 26
JF - PNAS
SN - 00278424
TI - Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses
VL - 114
ER -
TY - JOUR
AB - On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.
AU - Andrae, Magdalena
AU - Villányi, Márton
ID - 807
IS - 2
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
SN - 10222588
TI - Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung
VL - 70
ER -
TY - JOUR
AB - What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.
AU - Petritsch, Barbara
ID - 825
IS - 2
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
SN - 10222588
TI - Metadata for research data in practice
VL - 70
ER -
TY - GEN
AU - Schlögl, Alois
AU - Kiss, Janos
ID - 12905
T2 - AHPC17 – Austrian HPC Meeting 2017
TI - Scientific Computing at IST Austria
ER -
TY - JOUR
AB - The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement.
AU - Nanda, Gaurav
AU - Aguilera Servin, Juan L
AU - Rakyta, Péter
AU - Kormányos, Andor
AU - Kleiner, Reinhold
AU - Koelle, Dieter
AU - Watanabe, Kazuo
AU - Taniguchi, Takashi
AU - Vandersypen, Lieven
AU - Goswami, Srijit
ID - 988
IS - 6
JF - Nano Letters
SN - 15306984
TI - Current-phase relation of ballistic graphene Josephson junctions
VL - 17
ER -
TY - JOUR
AB - Actin filaments polymerizing against membranes power endocytosis, vesicular traffic, and cell motility. In vitro reconstitution studies suggest that the structure and the dynamics of actin networks respond to mechanical forces. We demonstrate that lamellipodial actin of migrating cells responds to mechanical load when membrane tension is modulated. In a steady state, migrating cell filaments assume the canonical dendritic geometry, defined by Arp2/3-generated 70° branch points. Increased tension triggers a dense network with a broadened range of angles, whereas decreased tension causes a shift to a sparse configuration dominated by filaments growing perpendicularly to the plasma membrane. We show that these responses emerge from the geometry of branched actin: when load per filament decreases, elongation speed increases and perpendicular filaments gradually outcompete others because they polymerize the shortest distance to the membrane, where they are protected from capping. This network-intrinsic geometrical adaptation mechanism tunes protrusive force in response to mechanical load.
AU - Mueller, Jan
AU - Szep, Gregory
AU - Nemethova, Maria
AU - De Vries, Ingrid
AU - Lieber, Arnon
AU - Winkler, Christoph
AU - Kruse, Karsten
AU - Small, John
AU - Schmeiser, Christian
AU - Keren, Kinneret
AU - Hauschild, Robert
AU - Sixt, Michael K
ID - 727
IS - 1
JF - Cell
SN - 00928674
TI - Load adaptation of lamellipodial actin networks
VL - 171
ER -
TY - JOUR
AB - We report the enhancement of infrared absorption of chemisorbed carbon monoxide on platinum in the gap of plasmonic nanoantennas. Our method is based on the self-assembled formation of platinum nanoislands on nanoscopic dipole antenna arrays manufactured via electron beam lithography. We employ systematic variations of the plasmonic antenna resonance to precisely couple to the molecular stretch vibration of carbon monoxide adsorbed on the platinum nanoislands. Ultimately, we reach more than 1500-fold infrared absorption enhancements, allowing for an ultrasensitive detection of a monolayer of chemisorbed carbon monoxide. The developed procedure can be adapted to other metal adsorbents and molecular species and could be utilized for coverage sensing in surface catalytic reactions.
AU - Haase, Johannes
AU - Bagiante, Salvatore
AU - Sigg, Hans
AU - Van Bokhoven, Jeroen
ID - 675
IS - 10
JF - Optics Letters
TI - Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas
VL - 42
ER -
TY - JOUR
AB - Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken.
AU - Villányi, Márton
ID - 1030
IS - 1
JF - Informationspraxis
SN - 2297-3249
TI - Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library
VL - 3
ER -
TY - DATA
AB - Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files.
AU - Hauschild, Robert
ID - 5570
KW - Cell migration
KW - tracking
KW - forward migration index
KW - FMI
TI - Forward migration indexes
ER -
TY - DATA
AB - This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity".
The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.
Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.
AU - Bergmiller, Tobias
AU - Andersson, Anna M
AU - Tomasek, Kathrin
AU - Balleza, Enrique
AU - Kiviet, Daniel
AU - Hauschild, Robert
AU - Tkacik, Gasper
AU - Guet, Calin C
ID - 5560
KW - single cell microscopy
KW - mother machine microfluidic device
KW - AcrAB-TolC pump
KW - multi-drug efflux
KW - Escherichia coli
TI - Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity
ER -
TY - JOUR
AB - The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria.
AU - Bergmiller, Tobias
AU - Andersson, Anna M
AU - Tomasek, Kathrin
AU - Balleza, Enrique
AU - Kiviet, Daniel
AU - Hauschild, Robert
AU - Tkacik, Gasper
AU - Guet, Calin C
ID - 665
IS - 6335
JF - Science
SN - 00368075
TI - Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity
VL - 356
ER -
TY - JOUR
AB - Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.
AU - Von Wangenheim, Daniel
AU - Hauschild, Robert
AU - Fendrych, Matyas
AU - Barone, Vanessa
AU - Benková, Eva
AU - Friml, Jirí
ID - 946
JF - eLife
TI - Live tracking of moving samples in confocal microscopy for vertically grown roots
VL - 6
ER -