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<title>bioRxiv Channel: Institute of Science and Technology Austria</title>
<link>https://biorxiv.org</link>
<description>
This feed contains articles for bioRxiv Channel "Institute of Science and Technology Austria"
</description>

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<prism:publicationName>bioRxiv</prism:publicationName>
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<title>bioRxiv</title>
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<link>https://biorxiv.org</link>
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<item rdf:about="https://biorxiv.org/content/10.1101/2024.09.20.614050v1?rss=1">
<title>
<![CDATA[
Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2024.09.20.614050v1?rss=1</link>
<description><![CDATA[
Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species.
]]></description>
<dc:creator>Vijatovic, D.</dc:creator>
<dc:creator>Toma, F. A.</dc:creator>
<dc:creator>Harrington, Z. P. M.</dc:creator>
<dc:creator>Sommer, C.</dc:creator>
<dc:creator>Hauschild, R.</dc:creator>
<dc:creator>Trevisan, A. J.</dc:creator>
<dc:creator>Chapman, P.</dc:creator>
<dc:creator>Julseth, M. J.</dc:creator>
<dc:creator>Brenner-Morton, S.</dc:creator>
<dc:creator>Gabitto, M. I.</dc:creator>
<dc:creator>Dasen, J. S.</dc:creator>
<dc:creator>Bikoff, J. B.</dc:creator>
<dc:creator>Sweeney, L. B.</dc:creator>
<dc:date>2024-09-21</dc:date>
<dc:identifier>doi:10.1101/2024.09.20.614050</dc:identifier>
<dc:title><![CDATA[Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2024-09-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2024.10.18.619072v1?rss=1">
<title>
<![CDATA[
Stability vs flexibility: reshaping monolayer and bilayer archaeal membranes in silico 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2024.10.18.619072v1?rss=1</link>
<description><![CDATA[
Cellular membranes differ across the tree of life. In most bacteria and eukaryotes, single-headed lipids self-assemble into flexible bilayer membranes. By contrast, thermophilic archaea tend to possess bilayer lipids together with double-headed, monolayer spanning bolalipids, which are thought to enable cells to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we explore the trade-offs at play when forming membranes. We find that flexible bolalipids form membranes that resemble bilayer membranes because they are able to assume a U-shaped conformation. Conversely, rigid bolalipids, which resemble the bolalipids with cyclic groups found in thermophilic archaea, take on a straight conformation and form membranes that are stiff and prone to pore formation when they undergo changes in shape. Strikingly, however, the inclusion of small amounts of bilayer lipids in a bolalipid membrane is enough to achieve fluid bolalipid membranes that are both stable and flexible - resolving this trade-off. Our study suggests a mechanism by which archaea can tune the material properties of their membranes as and when required to enable them to survive in harsh environments and to undergo essential membrane remodelling events like cell division.
]]></description>
<dc:creator>Amaral, M.</dc:creator>
<dc:creator>Frey, F.</dc:creator>
<dc:creator>Jiang, X.</dc:creator>
<dc:creator>Baum, B.</dc:creator>
<dc:creator>Saric, A.</dc:creator>
<dc:date>2024-10-20</dc:date>
<dc:identifier>doi:10.1101/2024.10.18.619072</dc:identifier>
<dc:title><![CDATA[Stability vs flexibility: reshaping monolayer and bilayer archaeal membranes in silico]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2024-10-20</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2025.06.27.661541v1?rss=1">
<title>
<![CDATA[
Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2025.06.27.661541v1?rss=1</link>
<description><![CDATA[
Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low-copy plasmids. In multicellular cyanobacteria like Anabaena sp., we found that a chromosomally-encoded ParMR has evolved into a novel cytoskeleton-termed CorMR-with a function in cell shape control rather than DNA segregation. Using live-cell imaging, in vitro reconstitution and Cryo-EM, we demonstrate that CorM forms dynamically unstable, antiparallel double-stranded filaments, which are recruited to the membrane by CorR via an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments are regulated by MinC, which excludes them from the poles and division plane. Comparative genomics reveal that the repurposing of ParMR and Min systems co-evolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria.
]]></description>
<dc:creator>Springstein, B. L.</dc:creator>
<dc:creator>Javoor, M. G.</dc:creator>
<dc:creator>Megrian, D.</dc:creator>
<dc:creator>Hajdu, R.</dc:creator>
<dc:creator>Hanke, D. M.</dc:creator>
<dc:creator>Loose, M.</dc:creator>
<dc:creator>Schur, F. K.</dc:creator>
<dc:date>2025-06-29</dc:date>
<dc:identifier>doi:10.1101/2025.06.27.661541</dc:identifier>
<dc:title><![CDATA[Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2025-06-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2025.08.11.669637v1?rss=1">
<title>
<![CDATA[
ALTAA: analysis of long-term activity patterns in ant colonies 
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</title>
<link>https://biorxiv.org/content/10.1101/2025.08.11.669637v1?rss=1</link>
<description><![CDATA[
Collective behaviours are a fascinating study area due to the emergent properties that can only arise in groups of interacting individuals. However, their quantitative study is often impaired by technical difficulties, creating either low-quality and sparse data, or impractical data amounts, particularly when capturing large groups over long periods of time. Common challenges arise from recording group members with as little obscuring of each other as possible, as well as in generating manageable data amounts with as high as possible information content. We here provide a multi-component system that allows to record, analyze and simulate the long-term spatiotemporal activity patterns of insect collectives, especially ant colonies. Our Ant Observing System, ALTAA, comprises a flat nest design to prevent occlusion of individuals, a recording system running on a low-power single-board-computer, and a set of computer programs performing quantitative analyses to guide the formation and validation of rules underlying the observed collective patterns. Our system is scalable in that it allows parallel, continuous observation of a high number of colonies using low memory space, with colony maintenance requirements (e.g. feeding, nest humidity) being achieved at lowest possible disturbance by the experimenter. We showcase the potential of the system in a study using the black garden ant, Lasius niger, where we analyze the spatiotemporal effects of different group size (1, 6, 10 ants), brood (larvae) presence or absence, as well as of different nest geometries, over a period of one week. We show that the ants motion activity has a weak periodicity in the range of 20 to 120 minutes promoted by larval presence, and that ants are spatially attracted to their larvae, the water source and the walls. We also find that the presence of nestmates lowers an individual ants motion activity. Observed data are compared to simulations of the temporal activity of the ants. ALTAA provides a powerful toolkit to quantify and interpret spatial and temporal collective activity patterns in (social) insects over extended periods.
]]></description>
<dc:creator>Oh, J.</dc:creator>
<dc:creator>Cremer, S.</dc:creator>
<dc:date>2025-08-12</dc:date>
<dc:identifier>doi:10.1101/2025.08.11.669637</dc:identifier>
<dc:title><![CDATA[ALTAA: analysis of long-term activity patterns in ant colonies]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2025-08-12</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2025.09.04.674342v1?rss=1">
<title>
<![CDATA[
Tandem association of CLOCK:BMAL1 complexes on DNA enables recruitment of CBP/p300 through multivalent interactions 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2025.09.04.674342v1?rss=1</link>
<description><![CDATA[
The basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) transcription factor CLOCK:BMAL1 interacts with E-box motifs in the context of nucleosomes to elicit a circadian pattern of gene expression that oscillates with approximately 24 hour periodicity. Core clock genes and other highly rhythmic targets of CLOCK:BMAL1 typically possess a tandem arrangement of E-boxes that is required for robust oscillations. Here, we show that the presence of tandem E-boxes enables CLOCK:BMAL1 to bind more internal sites on the nucleosome, leading to release of DNA from the histone core and the presentation of multiple coactivator binding motifs in close proximity to facilitate multivalent interactions with the coactivator CBP/p300. We show that the transactivation domain (TAD) of BMAL1, essential for CLOCK:BMAL1 activity, interacts with several modular domains of CBP. Deletion of these CBP domains or chemical inhibition of protein-protein interactions with CBP significantly reduces or eliminates CLOCK:BMAL1-driven activity. Altogether, this suggests that multivalent interactions with CBP may play a role in the ability of tandem CLOCK:BMAL1 heterodimers to recruit this limiting cofactor in cells.
]]></description>
<dc:creator>Sharma, D.</dc:creator>
<dc:creator>Stoos, L.</dc:creator>
<dc:creator>Torgrimson, M. R.</dc:creator>
<dc:creator>Crosby, P.</dc:creator>
<dc:creator>Franks, K. M.</dc:creator>
<dc:creator>Parsley, N. C.</dc:creator>
<dc:creator>Membreno, M.</dc:creator>
<dc:creator>Kempf, G.</dc:creator>
<dc:creator>Kater, L.</dc:creator>
<dc:creator>Gustafson, C. L.</dc:creator>
<dc:creator>Lee, H.-W.</dc:creator>
<dc:creator>Rubin, S.</dc:creator>
<dc:creator>Michael, A. K.</dc:creator>
<dc:creator>Thoma, N. H.</dc:creator>
<dc:creator>Partch, C. L.</dc:creator>
<dc:date>2025-09-07</dc:date>
<dc:identifier>doi:10.1101/2025.09.04.674342</dc:identifier>
<dc:title><![CDATA[Tandem association of CLOCK:BMAL1 complexes on DNA enables recruitment of CBP/p300 through multivalent interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2025-09-07</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2025.10.07.680881v1?rss=1">
<title>
<![CDATA[
MAKR6 targets TMK and CAMEL-CANAR receptor complexes for auxin canalization in Arabidopsis 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2025.10.07.680881v1?rss=1</link>
<description><![CDATA[
Adaptive plant development is orchestrated, among others, by directional, intercellular transport of the phytohormone auxin. Self-organizing development, such as flexible vasculature formation, depends on the auxin canalization manifested by the gradual formation of auxin transport channels via the feedback between auxin signalling and transport. Herein, we identify MAKR6 as a key, novel component of this feedback. MAKR6 expression highly accumulates in vascular cells and is tightly regulated by auxin via the Aux/IAA-ARF-WRKY23 transcriptional network. MAKR6 is indispensable for auxin canalization-dependent processes including leaf venation, vasculature regeneration, and de novo auxin channel formation from the local auxin sources. Mechanistically, MAKR6 directly interacts with the PIN1 auxin transporter to modulate its trafficking and polarization. MAKR6 also associates with and links two key receptor-like kinase (RLK) complexes involved in canalization, TMK1/4 and the CAMEL-CANAR. Together, our study establishes MAKR6 as a multifaceted regulator that couples transcriptional auxin signalling to PIN1 repolarization and coordinates multiple RLK-mediated signalling pathways in canalization. This provides mechanistic insights into auxin canalization and exemplifies a framework for exploring similar regulatory nodes in other developmental contexts.
]]></description>
<dc:creator>Ge, Z.</dc:creator>
<dc:creator>Koczka, L.</dc:creator>
<dc:creator>Mazur, E.</dc:creator>
<dc:creator>Molnar, G.</dc:creator>
<dc:creator>Ait Ikene, S.</dc:creator>
<dc:creator>Friml, J.</dc:creator>
<dc:date>2025-10-07</dc:date>
<dc:identifier>doi:10.1101/2025.10.07.680881</dc:identifier>
<dc:title><![CDATA[MAKR6 targets TMK and CAMEL-CANAR receptor complexes for auxin canalization in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2025-10-07</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2025.10.15.682552v1?rss=1">
<title>
<![CDATA[
Non-canonical cytokinesis driven by mechanical uncoupling via nematic flows and adhesion-based invagination 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2025.10.15.682552v1?rss=1</link>
<description><![CDATA[
Cleavage - the series of rapid cell divisions that follow fertilization - marks the onset of metazoan development and represents a deeply conserved evolutionary process. Across animals, two principal modes exist: complete (holoblastic) and incomplete (meroblastic) cleavage. While holoblastic cleavage resembles conventional cytokinesis both in vitro and in vivo, the mechanisms underlying meroblastic cleavage have remained poorly understood. Using zebrafish embryos as a model, we show that meroblastic cleavage proceeds through a distinct two-step mechanism. The process begins with the assembly and contraction of a large, arc-shaped actomyosin cable. However, this contractile event alone is insufficient to complete division. A second phase, driven by cadherin-mediated membrane adhesion, is required to invaginate the furrow ridge. Strikingly, this transition depends on mechanical uncoupling of the contractile cable from the surrounding cortex. We demonstrate that such uncoupling arises from an active nematic instability, which both enhances contractility along the cable and generates actin depletion zones that relieve lateral connections. Together, these findings reveal that meroblastic cleavage is governed not by a single actomyosin-based event but by a sequential interplay between cytoskeletal contraction and cadherin-dependent adhesion, highlighting a mechanism fundamentally distinct from canonical cytokinesis.
]]></description>
<dc:creator>Tong, X.</dc:creator>
<dc:creator>Li, Y. I.</dc:creator>
<dc:creator>Schelle, J.</dc:creator>
<dc:creator>Hannezo, E.</dc:creator>
<dc:creator>Heisenberg, C.-P.</dc:creator>
<dc:date>2025-10-15</dc:date>
<dc:identifier>doi:10.1101/2025.10.15.682552</dc:identifier>
<dc:title><![CDATA[Non-canonical cytokinesis driven by mechanical uncoupling via nematic flows and adhesion-based invagination]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2025-10-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.1101/2025.11.30.690169v1?rss=1">
<title>
<![CDATA[
Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota) 
]]>
</title>
<link>https://biorxiv.org/content/10.1101/2025.11.30.690169v1?rss=1</link>
<description><![CDATA[
Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1-3. Asgard archaea (phylum Promethearchaeota) which are considered the closest known prokaryotic relatives of eukaryotes potentially encode these functions within their large set of  eukaryotic signature proteins4-9. The few cultivated members show a complex cell morphology, consisting of a central cell body from which several protrusions extend, filled with an actin-based cytoskeleton10,11. Here, live cell microscopy of two organisms of the Loki- and Hodarchaea lineages10,12 showed that they dynamically and drastically change their cell shape on a minute time scale and grow and retract their extensive protrusions with a speed of 1.5 to 5.3 {micro}m/min, respectively. After adhering to a glass surface, cells employ their protrusions to undergo active crawling motion. In the presence of selected actin inhibitors however, the observed dynamics were arrested, suggesting a central role of actin in these processes. The observed cellular plasticity and motility are unique features among prokaryotes and might have been crucial for the emergence of the first eukaryotic cells that are thought to have formed through the association of a member of the Promethearchaeota and an alphaproteobacterium, the ancestor of mitochondria.
]]></description>
<dc:creator>Radler, P.</dc:creator>
<dc:creator>Viehboeck, T.</dc:creator>
<dc:creator>Luo, Z. H.</dc:creator>
<dc:creator>Maslac, N.</dc:creator>
<dc:creator>Schmidt, K.</dc:creator>
<dc:creator>Hauschild, R.</dc:creator>
<dc:creator>Nobu, M.</dc:creator>
<dc:creator>Bulgheresi, S.</dc:creator>
<dc:creator>Stradal, T. E. B.</dc:creator>
<dc:creator>Imachi, H.</dc:creator>
<dc:creator>Rottner, K.</dc:creator>
<dc:creator>Sixt, M.</dc:creator>
<dc:creator>Schleper, C.</dc:creator>
<dc:date>2025-12-01</dc:date>
<dc:identifier>doi:10.1101/2025.11.30.690169</dc:identifier>
<dc:title><![CDATA[Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2025-12-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://biorxiv.org/content/10.64898/2026.01.07.698144v1?rss=1">
<title>
<![CDATA[
Design and self-assembly of cytomotive filaments 
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</title>
<link>https://biorxiv.org/content/10.64898/2026.01.07.698144v1?rss=1</link>
<description><![CDATA[
Cytomotive filaments, a prominent class of cytoskeletal polymers comprising the actin and tubulin families, combine directional growth with monomer turnover to perform essential cellular functions. While the functional role of turnover is becoming increasingly clear, how these filaments dynamically self-assemble using a single monomer type remains an open question. Here we exploit physical modelling in combination with genetic algorithms to elucidate the design principles that drive monomer self-assembly into treadmilling filaments - polar filaments that grow on one end and shrink on the other. We first show that directional polymer growth is only possible when a structurally polar monomer changes conformation upon polymerisation, and identify three different mechanisms through which the structural polarity of a monomer can induce kinetic polarity. We then prove that to prevent filament fragmentation and promote end depolymerisation upon nucleotide hydrolysis, the conformation change of a polar monomer must involve both its interface-forming sites. Combining these results, we identify the principles required to design treadmilling monomers, and showcase the emergence of treadmilling dynamics from the bottom-up. Our work sheds light on the physical mechanisms underlying cytomotive self-assembly of biological polymers, and lays the base for the realization of essential cytoskeletal features in synthetic systems with programmable building blocks.
]]></description>
<dc:creator>Vanhille Campos, C.</dc:creator>
<dc:creator>Krstic, M.</dc:creator>
<dc:creator>Baum, B.</dc:creator>
<dc:creator>Munoz-Basagoiti, M.</dc:creator>
<dc:creator>Saric, A.</dc:creator>
<dc:date>2026-01-07</dc:date>
<dc:identifier>doi:10.64898/2026.01.07.698144</dc:identifier>
<dc:title><![CDATA[Design and self-assembly of cytomotive filaments]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory Press</dc:publisher>
<prism:publicationDate>2026-01-07</prism:publicationDate>
<prism:section></prism:section>
</item>
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