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Lennart J. Schulze, Sachin K. T. Veettil, Ivo F. Sbalzarini
A high-order fully Lagrangian particle level-set method for dynamic surfaces.
J Comput Phys, 515 Art. No. 113262 (2024)
Open Access   Source   

We present a fully Lagrangian particle level-set method based on high-order polynomial regression. This enables meshfree simulations of dynamic surfaces, relaxing the need for particle-mesh interpolation. Instead, we perform level-set redistancing directly on irregularly distributed particles by polynomial regression in a Newton-Lagrange basis on a set of unisolvent nodes. We demonstrate that the resulting particle closest-point (PCP) redistancing achieves high-order accuracy for 2D and 3D geometries discretized on irregular particle distributions and has better robustness against particle distortion than regression in a monomial basis. Further, we show convergence in classic level-set benchmark cases involving ill-conditioned particle distributions, and we present an example application to multi-phase flow problems involving oscillating and dividing droplets.
@article{Schulze8766,
author={Lennart J. Schulze, Sachin K. T. Veettil, Ivo F. Sbalzarini},
title={A high-order fully Lagrangian particle level-set method for dynamic surfaces.},
journal ={Journal of Computational Physics},
volume={515},
pages={null--null},
year=2024
}

David Thomas Gonzales, Naresh Yandrapalli, Tom Robinson, Christoph Zechner#, T-Y Dora Tang#
Correction to "Cell-Free Gene Expression Dynamics in Synthetic Cell Populations".
ACS Synth Biol, Art. No. doi: 10.1021/acssynbio.4c00583 (2024)
Open Access PubMed Source  

@article{Gonzales8811,
author={David Thomas Gonzales, Naresh Yandrapalli, Tom Robinson, Christoph Zechner, T-Y Dora Tang},
title={Correction to "Cell-Free Gene Expression Dynamics in Synthetic Cell Populations".},
journal ={ACS synthetic biology},
volume={},
pages={1--1},
year=2024
}

Takashi Namba, Wieland Huttner
What Makes Us Human: Insights from the Evolution and Development of the Human Neocortex.
Annu Rev Cell Dev Biol, 40(1) 427-452 (2024)
Open Access PubMed Source   

"What makes us human?" is a central question of many research fields, notably anthropology. In this review, we focus on the development of the human neocortex, the part of the brain with a key role in cognition, to gain neurobiological insight toward answering this question. We first discuss cortical stem and progenitor cells and human-specific genes that affect their behavior. We thus aim to understand the molecular foundation of the expansion of the neocortex that occurred in the course of human evolution, as this expansion is generally thought to provide a basis for our unique cognitive abilities. We then review the emerging evidence pointing to differences in the development of the neocortex between present-day humans and Neanderthals, our closest relatives. Finally, we discuss human-specific genes that have been implicated in neuronal circuitry and offer a perspective for future studies addressing the question of what makes us human.
@article{Namba8810,
author={Takashi Namba, Wieland Huttner},
title={What Makes Us Human: Insights from the Evolution and Development of the Human Neocortex.},
journal ={Annual review of cell and developmental biology},
volume={40},
issue ={1},
pages={427--452},
year=2024
}

Manfred Schartl#, Joost M Woltering, Iker Irisarri, Kang Du, Susanne Kneitz, Martin Pippel, Thomas Brown, Paolo Franchini, Jing Li, Ming Li, Mateus Adolfi, Sylke Winkler, Josane de Freitas Sousa, Zhuoxin Chen, Sandra Jacinto, Evgeny Z Kvon, Luis Rogério Correa de Oliveira, Erika Monteiro, Danielson Baia Amaral, Thorsten Burmester, Domitille Chalopin, Alexander Suh, Eugene W Myers, Oleg Simakov, Igor Schneider, Axel Meyer#
The genomes of all lungfish inform on genome expansion and tetrapod evolution.
Nature, 634(8032) 96-103 (2024)
PubMed Source   

The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
@article{Schartl8782,
author={Manfred Schartl, Joost M Woltering, Iker Irisarri, Kang Du, Susanne Kneitz, Martin Pippel, Thomas Brown, Paolo Franchini, Jing Li, Ming Li, Mateus Adolfi, Sylke Winkler, Josane de Freitas Sousa, Zhuoxin Chen, Sandra Jacinto, Evgeny Z Kvon, Luis Rogério Correa de Oliveira, Erika Monteiro, Danielson Baia Amaral, Thorsten Burmester, Domitille Chalopin, Alexander Suh, Eugene W Myers, Oleg Simakov, Igor Schneider, Axel Meyer},
title={The genomes of all lungfish inform on genome expansion and tetrapod evolution.},
journal ={Nature},
volume={634},
issue ={8032},
pages={96--103},
year=2024
}

Heidi L van de Wouw, Shuo-Ting Yen, Manon Valet, Joseph A Garcia, Carlos O Gomez, Antoine Vian, Yucen Liu, Jennifer Pollock, Petr Pospíšil, Otger Campàs, Ellen M Sletten
Non-Ionic Fluorosurfactants for Droplet-Based in vivo Applications.
Angew Chem Int Ed Engl, Art. No. doi: 10.1002/anie.202404956 (2024)
PubMed Source   

Fluorocarbon oils are uniquely suited for many biomedical applications due to their inert, bioorthogonal properties. In order to interface fluorocarbon oils with biological systems, non-ionic fluorosurfactants are necessary. However, there is a paucity of non-ionic fluorosurfactants with low interfacial tension to stabilize fluorocarbon phases in aqueous environments (such as oil-in-water emulsions). We developed non-ionic fluorosurfactants composed of a polyethylene glycol (PEG) segment covalently bonded to a flexible perfluoropolyether (PFPE) segment that confer lower interfacial tensions (IFTs) between a fluorocarbon oil, HFE-7700, and water. Synthesis of a panel of surfactants spanning a molecular weight range of 0.64-66 kDa with various hydrophilic-lipophilic balances allowed for identification of minimal IFTs, ranging from 1.4 to 17.8 mN m-1. The majority of these custom fluorosurfactants display poor solubility in water, allowing their co-introduction with fluorocarbon oils and minimal leaching. We applied the PEG5PFPE1 surfactant for mechanical force measurements in zebrafish, enabling exceptional sensitivity.
@article{Wouw8808,
author={Heidi L van de Wouw, Shuo-Ting Yen, Manon Valet, Joseph A Garcia, Carlos O Gomez, Antoine Vian, Yucen Liu, Jennifer Pollock, Petr Pospíšil, Otger Campàs, Ellen M Sletten},
title={Non-Ionic Fluorosurfactants for Droplet-Based in vivo Applications.},
journal ={Angewandte Chemie (International ed. in English)},
volume={},
pages={1--1},
year=2024
}

Oliver Kutz, Stephan Drukewitz, Alexander Krüger, Daniela Aust, Doreen William, Sandra Oster, Evelin Schröck, Gustavo Baretton, Theresa Link, Pauline Wimberger, Jan Dominik Kuhlmann
Exploring evolutionary trajectories in ovarian cancer patients by longitudinal analysis of ctDNA.
Clin Chem Lab Med, 62(10) 2070-2081 (2024)
PubMed Source   

We analysed whether temporal heterogeneity of ctDNA encodes evolutionary patterns in ovarian cancer.
@article{Kutz8701,
author={Oliver Kutz, Stephan Drukewitz, Alexander Krüger, Daniela Aust, Doreen William, Sandra Oster, Evelin Schröck, Gustavo Baretton, Theresa Link, Pauline Wimberger, Jan Dominik Kuhlmann},
title={Exploring evolutionary trajectories in ovarian cancer patients by longitudinal analysis of ctDNA.},
journal ={Clinical chemistry and laboratory medicine},
volume={62},
issue ={10},
pages={2070--2081},
year=2024
}

Metin G Davutoglu, Veikko Geyer, Lukas Niese, Johannes R Soltwedel, Marcelo L Zoccoler, Valeria Sabatino, Robert Haase, Nils Kröger, Stefan Diez#, Nicole Poulsen#
Gliding motility of the diatom Craspedostauros australis coincides with the intracellular movement of raphid-specific myosins.
Commun Biol, 7(1) Art. No. 1187 (2024)
Open Access PubMed Source Full Text   

Raphid diatoms are one of the few eukaryotes capable of gliding motility, which is remarkably fast and allows for quasi-instantaneous directional reversals. Besides other mechanistic models, it has been suggested that an actomyosin system provides the force for diatom gliding. However, in vivo data on the dynamics of actin and myosin in diatoms are lacking. In this study, we demonstrate that the raphe-associated actin bundles required for diatom movement do not exhibit a directional turnover of subunits and thus their dynamics do not contribute directly to force generation. By phylogenomic analysis, we identified four raphid diatom-specific myosins in Craspedostauros australis (CaMyo51A-D) and investigated their in vivo localization and dynamics through GFP-tagging. Only CaMyo51B-D but not CaMyo51A exhibited coordinated movement during gliding, consistent with a role in force generation. The characterization of raphid diatom-specific myosins lays the foundation for unraveling the molecular mechanisms that underlie the gliding motility of diatoms.
@article{Davutoglu8807,
author={Metin G Davutoglu, Veikko Geyer, Lukas Niese, Johannes R Soltwedel, Marcelo L Zoccoler, Valeria Sabatino, Robert Haase, Nils Kröger, Stefan Diez, Nicole Poulsen},
title={Gliding motility of the diatom Craspedostauros australis coincides with the intracellular movement of raphid-specific myosins.},
journal ={Communications biology},
volume={7},
issue ={1},
pages={null--null},
year=2024
}

Mario Ivanković✳︎, Jeremias N Brand✳︎, Luca Pandolfini, Thomas Brown, Martin Pippel, Andrei Rozanski, Til Schubert, Markus Grohme, Sylke Winkler, Laura Robledillo, Meng Zhang, Azzurra Codino, Stefano Gustincich, Miquel Vila-Farré, Shu Zhang, Argyris Papantonis, André Marques, Jochen Rink
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.
Nat Commun, 15(1) Art. No. 8215 (2024)
Open Access PubMed Source Full Text   

The planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.
@article{Ivanković8801,
author={Mario Ivanković, Jeremias N Brand, Luca Pandolfini, Thomas Brown, Martin Pippel, Andrei Rozanski, Til Schubert, Markus Grohme, Sylke Winkler, Laura Robledillo, Meng Zhang, Azzurra Codino, Stefano Gustincich, Miquel Vila-Farré, Shu Zhang, Argyris Papantonis, André Marques, Jochen Rink},
title={A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.},
journal ={Nature communications},
volume={15},
issue ={1},
pages={null--null},
year=2024
}

Rahul M Sarate✳︎, Joel Hochstetter✳︎, Manon Valet✳︎, Adrien Hallou, Yura Song, Nordin Bansaccal, Melanie Ligare, Mariaceleste Aragona, Dan Engelman, Anaïs Bauduin, Otger Campàs#, Benjamin D Simons#, Cedric Blanpain#
Dynamic regulation of tissue fluidity controls skin repair during wound healing.
Cell, 187(19) 5298-5315 (2024)
Open Access PubMed Source   

During wound healing, different pools of stem cells (SCs) contribute to skin repair. However, how SCs become activated and drive the tissue remodeling essential for skin repair is still poorly understood. Here, by developing a mouse model allowing lineage tracing and basal cell lineage ablation, we monitor SC fate and tissue dynamics during regeneration using confocal and intravital imaging. Analysis of basal cell rearrangements shows dynamic transitions from a solid-like homeostatic state to a fluid-like state allowing tissue remodeling during repair, as predicted by a minimal mathematical modeling of the spatiotemporal dynamics and fate behavior of basal cells. The basal cell layer progressively returns to a solid-like state with re-epithelialization. Bulk, single-cell RNA, and epigenetic profiling of SCs, together with functional experiments, uncover a common regenerative state regulated by the EGFR/AP1 axis activated during tissue fluidization that is essential for skin SC activation and tissue repair.
@article{Sarate8789,
author={Rahul M Sarate, Joel Hochstetter, Manon Valet, Adrien Hallou, Yura Song, Nordin Bansaccal, Melanie Ligare, Mariaceleste Aragona, Dan Engelman, Anaïs Bauduin, Otger Campàs, Benjamin D Simons, Cedric Blanpain},
title={Dynamic regulation of tissue fluidity controls skin repair during wound healing.},
journal ={Cell},
volume={187},
issue ={19},
pages={5298--5315},
year=2024
}

Tomáš Takáč, Lenka Kuběnová, Olga Šamajová, Petr Dvořák, Jan Řehák, Jan Haberland, Sebastian T. Bundschuh, Tibor Pechan, Pavel Tomančák, Miroslav Ovečka, Jozef Šamaj
Actin cytoskeleton and plasma membrane aquaporins are involved in different drought response of Arabidopsis rhd2 and der1 root hair mutants.
Plant Physiol Biochem, 216 Art. No. 109137 (2024)
Open Access PubMed Source   

Actin cytoskeleton and reactive oxygen species are principal determinants of root hair polarity and tip growth. Loss of function in RESPIRATORY BURST OXIDASE HOMOLOG C/ROOT HAIR DEFECTIVE 2 (AtRBOHC/RHD2), an NADPH oxidase emitting superoxide to the apoplast, and in ACTIN 2, a vegetative actin isovariant, in rhd2-1 and der1-3 mutants, respectively, lead to similar defects in root hair formation and elongation Since early endosome-mediated polar localization of AtRBOHC/RHD2 depends on actin cytoskeleton, comparing the proteome-wide consequences of both mutations might be of eminent interest. Therefore, we employed a differential proteomic analysis of Arabidopsis rhd2-1 and der1-3 mutants. Both mutants exhibited substantial alterations in abundances of stress-related proteins. Notably, plasma membrane (PM)-localized PIP aquaporins showed contrasting abundance patterns in the mutants compared to wild-types. Drought-responsive proteins were mostly downregulated in rhd2-1 but upregulated in der1-3. Proteomic data suggest that opposite to der1-3, altered vesicular transport in rhd2-1 mutant likely contributes to the deregulation of PM-localized proteins, including PIPs. Moreover, lattice light sheet microscopy revealed reduced actin dynamics in rhd2-1 roots, a finding contrasting with previous reports on der1-3 mutant. Phenotypic experiments demonstrated a drought stress susceptibility in rhd2-1 and resistance in der1-3. Thus, mutations in AtRBOHC/RHD2 and ACTIN2 cause similar root hair defects, but they differently affect the actin cytoskeleton and vesicular transport. Reduced actin dynamics in rhd2-1 mutant is accompanied by alteration of vesicular transport proteins abundance, likely leading to altered protein delivery to PM, including aquaporins, thereby significantly affecting drought stress responses.
@article{Takáč8809,
author={Tomáš Takáč, Lenka Kuběnová, Olga Šamajová, Petr Dvořák, Jan Řehák, Jan Haberland, Sebastian T. Bundschuh, Tibor Pechan, Pavel Tomančák, Miroslav Ovečka, Jozef Šamaj},
title={Actin cytoskeleton and plasma membrane aquaporins are involved in different drought response of Arabidopsis rhd2 and der1 root hair mutants.},
journal ={Plant physiology and biochemistry : PPB},
volume={216},
pages={null--null},
year=2024
}
✳︎ joint first authors, # joint corresponding authors
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