@article{15262, author = {Ernst, Doris}, journal = {Today}, title = {{Doris Test 18.11.}}, year = {2024}, } @article{12158, abstract = {Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.}, author = {Zeller, Peter and Yeung, Jake and Viñas Gaza, Helena and de Barbanson, Buys Anton and Bhardwaj, Vivek and Florescu, Maria and van der Linden, Reinier and van Oudenaarden, Alexander}, issn = {1546-1718}, journal = {Nature Genetics}, keywords = {Genetics}, pages = {333--345}, publisher = {Springer Nature}, title = {{Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis}}, doi = {10.1038/s41588-022-01260-3}, volume = {55}, year = {2023}, } @article{12334, abstract = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.}, author = {Fäßler, Florian and Javoor, Manjunath and Datler, Julia and Döring, Hermann and Hofer, Florian and Dimchev, Georgi A and Hodirnau, Victor-Valentin and Faix, Jan and Rottner, Klemens and Schur, Florian KM}, issn = {2375-2548}, journal = {Science Advances}, keywords = {Multidisciplinary}, number = {3}, publisher = {American Association for the Advancement of Science}, title = {{ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning}}, doi = {10.1126/sciadv.add6495}, volume = {9}, year = {2023}, } @article{12543, abstract = {Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts.}, author = {Stock, Miriam and Milutinovic, Barbara and Hönigsberger, Michaela and Grasse, Anna V and Wiesenhofer, Florian and Kampleitner, Niklas and Narasimhan, Madhumitha and Schmitt, Thomas and Cremer, Sylvia}, issn = {2397-334X}, journal = {Nature Ecology and Evolution}, pages = {450--460}, publisher = {Springer Nature}, title = {{Pathogen evasion of social immunity}}, doi = {10.1038/s41559-023-01981-6}, volume = {7}, year = {2023}, } @article{12747, abstract = {Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.}, author = {Cikes, Domagoj and Elsayad, Kareem and Sezgin, Erdinc and Koitai, Erika and Ferenc, Torma and Orthofer, Michael and Yarwood, Rebecca and Heinz, Leonhard X. and Sedlyarov, Vitaly and Darwish-Miranda, Nasser and Taylor, Adrian and Grapentine, Sophie and al-Murshedi, Fathiya and Abot, Anne and Weidinger, Adelheid and Kutchukian, Candice and Sanchez, Colline and Cronin, Shane J. F. and Novatchkova, Maria and Kavirayani, Anoop and Schuetz, Thomas and Haubner, Bernhard and Haas, Lisa and Hagelkruys, Astrid and Jackowski, Suzanne and Kozlov, Andrey and Jacquemond, Vincent and Knauf, Claude and Superti-Furga, Giulio and Rullman, Eric and Gustafsson, Thomas and McDermot, John and Lowe, Martin and Radak, Zsolt and Chamberlain, Jeffrey S. and Bakovic, Marica and Banka, Siddharth and Penninger, Josef M.}, issn = {2522-5812}, journal = {Nature Metabolism}, keywords = {Cell Biology, Physiology (medical), Endocrinology, Diabetes and Metabolism, Internal Medicine}, pages = {495--515}, publisher = {Springer Nature}, title = {{PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing}}, doi = {10.1038/s42255-023-00766-2}, volume = {5}, year = {2023}, } @article{12830, abstract = {Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.}, author = {Huljev, Karla and Shamipour, Shayan and Nunes Pinheiro, Diana C and Preusser, Friedrich and Steccari, Irene and Sommer, Christoph M and Naik, Suyash and Heisenberg, Carl-Philipp J}, issn = {1878-1551}, journal = {Developmental Cell}, number = {7}, pages = {582--596.e7}, publisher = {Elsevier}, title = {{A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish}}, doi = {10.1016/j.devcel.2023.02.016}, volume = {58}, year = {2023}, } @article{12863, abstract = {In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.}, author = {Filipović Marijić, Vlatka and Krasnici, Nesrete and Valić, Damir and Kapetanović, Damir and Vardić Smrzlić, Irena and Jordanova, Maja and Rebok, Katerina and Ramani, Sheriban and Kostov, Vasil and Nastova, Rodne and Dragun, Zrinka}, issn = {1614-7499}, journal = {Environmental Science and Pollution Research}, pages = {63510--63521}, publisher = {Springer Nature}, title = {{Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish}}, doi = {10.1007/s11356-023-26844-2}, volume = {30}, year = {2023}, } @article{13033, abstract = {Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.}, author = {Zavadakova, Anna and Vistejnova, Lucie and Belinova, Tereza and Tichanek, Filip and Bilikova, Dagmar and Mouton, Peter R.}, issn = {2045-2322}, journal = {Scientific Reports}, keywords = {Multidisciplinary}, number = {1}, publisher = {Springer Nature}, title = {{Novel stereological method for estimation of cell counts in 3D collagen scaffolds}}, doi = {10.1038/s41598-023-35162-z}, volume = {13}, year = {2023}, } @article{13044, abstract = {Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation.}, author = {Mondal, Soumyadip and Jethwa, Rajesh B and Pant, Bhargavi and Hauschild, Robert and Freunberger, Stefan Alexander}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, publisher = {Royal Society of Chemistry}, title = {{Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes}}, doi = {10.1039/d3fd00088e}, year = {2023}, } @inbook{13052, abstract = {Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.}, author = {Leithner, Alexander F and Merrin, Jack and Sixt, Michael K}, booktitle = {The Immune Synapse}, editor = {Baldari, Cosima and Dustin, Michael}, isbn = {9781071631348}, issn = {1940-6029}, pages = {137--147}, publisher = {Springer Nature}, title = {{En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses}}, doi = {10.1007/978-1-0716-3135-5_9}, volume = {2654}, year = {2023}, } @misc{13126, abstract = {Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.}, author = {Danzl, Johann G}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for the publication "Imaging brain tissue architecture across millimeter to nanometer scales"}}, doi = {10.15479/AT:ISTA:13126}, year = {2023}, } @inproceedings{13161, author = {Schlögl, Alois and Elefante, Stefano and Hodirnau, Victor-Valentin}, booktitle = {ASHPC23 - Austrian-Slovenian HPC Meeting 2023}, location = {Maribor, Slovenia}, pages = {59--59}, publisher = {EuroCC}, title = {{Running Windows-applications on a Linux HPC cluster using WINE}}, year = {2023}, } @inproceedings{13162, author = {Elefante, Stefano and Stadlbauer, Stephan and Alexander, Michael F and Schlögl, Alois}, booktitle = {ASHPC23 - Austrian-Slovenian HPC Meeting 2023}, location = {Maribor, Slovenia}, pages = {42--42}, publisher = {EuroCC}, title = {{Cryo-EM software packages: A sys-admins point of view}}, year = {2023}, } @article{13267, abstract = {Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.}, author = {Velicky, Philipp and Miguel Villalba, Eder and Michalska, Julia M and Lyudchik, Julia and Wei, Donglai and Lin, Zudi and Watson, Jake and Troidl, Jakob and Beyer, Johanna and Ben Simon, Yoav and Sommer, Christoph M and Jahr, Wiebke and Cenameri, Alban and Broichhagen, Johannes and Grant, Seth G.N. and Jonas, Peter M and Novarino, Gaia and Pfister, Hanspeter and Bickel, Bernd and Danzl, Johann G}, issn = {1548-7105}, journal = {Nature Methods}, pages = {1256--1265}, publisher = {Springer Nature}, title = {{Dense 4D nanoscale reconstruction of living brain tissue}}, doi = {10.1038/s41592-023-01936-6}, volume = {20}, year = {2023}, } @unpublished{13312, abstract = {Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a $ \sin \left( 2 \varphi \right)$ CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with $ \approx 100 \%$ efficiency. The reported results open up the path towards monolithic integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on a silicon technology compatible platform.}, author = {Valentini, Marco and Sagi, Oliver and Baghumyan, Levon and Gijsel, Thijs de and Jung, Jason and Calcaterra, Stefano and Ballabio, Andrea and Servin, Juan Aguilera and Aggarwal, Kushagra and Janik, Marian and Adletzberger, Thomas and Souto, Rubén Seoane and Leijnse, Martin and Danon, Jeroen and Schrade, Constantin and Bakkers, Erik and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios}, booktitle = {arXiv}, keywords = {Mesoscale and Nanoscale Physics}, title = {{Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas}}, doi = {10.48550/arXiv.2306.07109}, year = {2023}, } @article{13342, abstract = {Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.}, author = {Kroll, Janina and Hauschild, Robert and Kuznetcov, Arthur and Stefanowski, Kasia and Hermann, Monika D. and Merrin, Jack and Shafeek, Lubuna B and Müller-Taubenberger, Annette and Renkawitz, Jörg}, issn = {1460-2075}, journal = {EMBO Journal}, publisher = {Embo Press}, title = {{Adaptive pathfinding by nucleokinesis during amoeboid migration}}, doi = {10.15252/embj.2023114557}, year = {2023}, } @article{14786, abstract = {Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species.}, author = {Filipović Marijić, Vlatka and Subirana, Maria Angels and Schaumlöffel, Dirk and Barišić, Josip and Gontier, Etienne and Krasnici, Nesrete and Mijošek, Tatjana and Hernández-Orts, Jesús S. and Scholz, Tomáš and Erk, Marijana}, issn = {0048-9697}, journal = {Science of The Total Environment}, keywords = {Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering}, publisher = {Elsevier}, title = {{First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS}}, doi = {10.1016/j.scitotenv.2023.164010}, volume = {887}, year = {2023}, } @article{14799, abstract = {A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.}, author = {Pauw, Brian R. and Smales, Glen J. and Anker, Andy S. and Annadurai, Venkatasamy and Balazs, Daniel and Bienert, Ralf and Bouwman, Wim G. and Breßler, Ingo and Breternitz, Joachim and Brok, Erik S. and Bryant, Gary and Clulow, Andrew J. and Crater, Erin R. and De Geuser, Frédéric and Giudice, Alessandra Del and Deumer, Jérôme and Disch, Sabrina and Dutt, Shankar and Frank, Kilian and Fratini, Emiliano and Garcia, Paulo R.A.F. and Gilbert, Elliot P. and Hahn, Marc B. and Hallett, James and Hohenschutz, Max and Hollamby, Martin and Huband, Steven and Ilavsky, Jan and Jochum, Johanna K. and Juelsholt, Mikkel and Mansel, Bradley W. and Penttilä, Paavo and Pittkowski, Rebecca K. and Portale, Giuseppe and Pozzo, Lilo D. and Rochels, Leonhard and Rosalie, Julian M. and Saloga, Patrick E.J. and Seibt, Susanne and Smith, Andrew J. and Smith, Gregory N. and Spiering, Glenn A. and Stawski, Tomasz M. and Taché, Olivier and Thünemann, Andreas F. and Toth, Kristof and Whitten, Andrew E. and Wuttke, Joachim}, issn = {1600-5767}, journal = {Journal of Applied Crystallography}, number = {6}, pages = {1618--1629}, title = {{The human factor: Results of a small-angle scattering data analysis round robin}}, doi = {10.1107/S1600576723008324}, volume = {56}, year = {2023}, } @article{14041, abstract = {Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.}, author = {Méhes, Elod and Mones, Enys and Varga, Máté and Zsigmond, Áron and Biri-Kovács, Beáta and Nyitray, László and Barone, Vanessa and Krens, Gabriel and Heisenberg, Carl-Philipp J and Vicsek, Tamás}, issn = {2399-3642}, journal = {Communications Biology}, publisher = {Springer Nature}, title = {{3D cell segregation geometry and dynamics are governed by tissue surface tension regulation}}, doi = {10.1038/s42003-023-05181-7}, volume = {6}, year = {2023}, } @article{14257, abstract = {Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.}, author = {Michalska, Julia M and Lyudchik, Julia and Velicky, Philipp and Korinkova, Hana and Watson, Jake and Cenameri, Alban and Sommer, Christoph M and Amberg, Nicole and Venturino, Alessandro and Roessler, Karl and Czech, Thomas and Höftberger, Romana and Siegert, Sandra and Novarino, Gaia and Jonas, Peter M and Danzl, Johann G}, issn = {1546-1696}, journal = {Nature Biotechnology}, publisher = {Springer Nature}, title = {{Imaging brain tissue architecture across millimeter to nanometer scales}}, doi = {10.1038/s41587-023-01911-8}, year = {2023}, }