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Hendrik Frentzel, Marco Kraemer, Ylanna Kelner-Burgos, Laura Uelze, Dorina Bodi
Cereulide production capacities and genetic properties of 31 emetic Bacillus cereus group strains.
Int J Food Microbiol, 417 Art. No. 110694 (2024)
Open Access PubMed Source   

The highly potent toxin cereulide is a frequent cause of foodborne intoxications. This extremely resistant toxin is produced by Bacillus cereus group strains carrying the plasmid encoded cesHPTABCD gene cluster. It is known that the capacities to produce cereulide vary greatly between different strains but the genetic background of these variations is not clear. In this study, cereulide production capacities were associated with genetic characteristics. For this, cereulide levels in cultures of 31 strains were determined after incubation in tryptic soy broth for 24 h at 24 °C, 30 °C and 37 °C. Whole genome sequencing based data were used for an in-depth characterization of gene sequences related to cereulide production. The taxonomy, population structure and phylogenetic relationships of the strains were evaluated based on average nucleotide identity, multi-locus sequence typing (MLST), core genome MLST and single nucleotide polymorphism analyses. Despite a limited strain number, the approach of a genome wide association study (GWAS) was tested to link genetic variation with cereulide quantities. Our study confirms strain-dependent differences in cereulide production. For most strains, these differences were not explainable by sequence variations in the cesHPTABCD gene cluster or the regulatory genes abrB, spo0A, codY and pagRBc. Likewise, the population structure and phylogeny of the tested strains did not comprehensively reflect the cereulide production capacities. GWAS yielded first hints for associated proteins, while their possible effect on cereulide synthesis remains to be further investigated.
@article{Frentzel8707,
author={Hendrik Frentzel, Marco Kraemer, Ylanna Kelner-Burgos, Laura Uelze, Dorina Bodi},
title={Cereulide production capacities and genetic properties of 31 emetic Bacillus cereus group strains.},
journal ={International journal of food microbiology},
volume={417},
pages={null--null},
year=2024
}

Christine Desroches Altamirano, Moo-Koo Kang, Mareike A Jordan, Tom Borianne, Irem Dilmen, Maren Gnädig, Alexander von Appen, Alf Honigmann, Titus Franzmann, Simon Alberti
eIF4F is a thermo-sensing regulatory node in the translational heat shock response.
Mol Cell, 84(9) 1727-1741 (2024)
Open Access PubMed Source   

Heat-shocked cells prioritize the translation of heat shock (HS) mRNAs, but the underlying mechanism is unclear. We report that HS in budding yeast induces the disassembly of the eIF4F complex, where eIF4G and eIF4E assemble into translationally arrested mRNA ribonucleoprotein particles (mRNPs) and HS granules (HSGs), whereas eIF4A promotes HS translation. Using in vitro reconstitution biochemistry, we show that a conformational rearrangement of the thermo-sensing eIF4A-binding domain of eIF4G dissociates eIF4A and promotes the assembly with mRNA into HS-mRNPs, which recruit additional translation factors, including Pab1p and eIF4E, to form multi-component condensates. Using extracts and cellular experiments, we demonstrate that HS-mRNPs and condensates repress the translation of associated mRNA and deplete translation factors that are required for housekeeping translation, whereas HS mRNAs can be efficiently translated by eIF4A. We conclude that the eIF4F complex is a thermo-sensing node that regulates translation during HS.
@article{Altamirano8704,
author={Christine Desroches Altamirano, Moo-Koo Kang, Mareike A Jordan, Tom Borianne, Irem Dilmen, Maren Gnädig, Alexander von Appen, Alf Honigmann, Titus Franzmann, Simon Alberti},
title={eIF4F is a thermo-sensing regulatory node in the translational heat shock response.},
journal ={Molecular cell},
volume={84},
issue ={9},
pages={1727--1741},
year=2024
}

Carlos M Duque, Douglas M Hall, Botond Tyukodi, Michael F Hagan, Christian D Santangelo, Gregory M Grason
Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra.
Proc Natl Acad Sci U.S.A., 121(18) Art. No. e2315648121 (2024)
Open Access PubMed Source   

We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.
@article{Duque8711,
author={Carlos M Duque, Douglas M Hall, Botond Tyukodi, Michael F Hagan, Christian D Santangelo, Gregory M Grason},
title={Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={121},
issue ={18},
pages={null--null},
year=2024
}

Lei Xing#, Vasiliki Gkini, Anni I Nieminen, Hui-Chao Zhou, Matilde Aquilino, Ronald Naumann, Katrin Reppe, Kohichi Tanaka, Peter Carmeliet, Oskari Heikinheimo, Svante Pääbo, Wieland Huttner#, Takashi Namba#
Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development.
Nat Commun, 15(1) Art. No. 3468 (2024)
Open Access PubMed Source   

Metabolism has recently emerged as a major target of genes implicated in the evolutionary expansion of human neocortex. One such gene is the human-specific gene ARHGAP11B. During human neocortex development, ARHGAP11B increases the abundance of basal radial glia, key progenitors for neocortex expansion, by stimulating glutaminolysis (glutamine-to-glutamate-to-alpha-ketoglutarate) in mitochondria. Here we show that the ape-specific protein GLUD2 (glutamate dehydrogenase 2), which also operates in mitochondria and converts glutamate-to-αKG, enhances ARHGAP11B's ability to increase basal radial glia abundance. ARHGAP11B + GLUD2 double-transgenic bRG show increased production of aspartate, a metabolite essential for cell proliferation, from glutamate via alpha-ketoglutarate and the TCA cycle. Hence, during human evolution, a human-specific gene exploited the existence of another gene that emerged during ape evolution, to increase, via concerted changes in metabolism, progenitor abundance and neocortex size.
@article{Xing8710,
author={Lei Xing, Vasiliki Gkini, Anni I Nieminen, Hui-Chao Zhou, Matilde Aquilino, Ronald Naumann, Katrin Reppe, Kohichi Tanaka, Peter Carmeliet, Oskari Heikinheimo, Svante Pääbo, Wieland Huttner, Takashi Namba},
title={Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development.},
journal ={Nature communications},
volume={15},
issue ={1},
pages={null--null},
year=2024
}

Cristina Cacho-Navas, Carmen López-Pujante, Natalia Reglero-Real, Natalia Colás-Algora, A Cuervo, Jose Javier Conesa, Susana Barroso, Gema de Rivas, Sergio Ciordia, Alberto Paradela, Gianluca D'Agostino, Carlo Manzo, Jorge Feito, Germán Andrés, Francisca Molina-Jiménez, Pedro Majano, Isabel Correas, J M Carazo, Sussan Nourshargh, Meritxell Huch, Jaime Millán
ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin.
Elife, 12 Art. No. RP89261 (2024)
Open Access PubMed Source   

Epithelial intercellular adhesion molecule (ICAM)-1 is apically polarized, interacts with, and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1_KO human hepatic cells, liver organoids from ICAM-1_KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures. We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress.
@article{Cacho-Navas8708,
author={Cristina Cacho-Navas, Carmen López-Pujante, Natalia Reglero-Real, Natalia Colás-Algora, A Cuervo, Jose Javier Conesa, Susana Barroso, Gema de Rivas, Sergio Ciordia, Alberto Paradela, Gianluca D'Agostino, Carlo Manzo, Jorge Feito, Germán Andrés, Francisca Molina-Jiménez, Pedro Majano, Isabel Correas, J M Carazo, Sussan Nourshargh, Meritxell Huch, Jaime Millán},
title={ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin.},
journal ={eLife},
volume={12},
pages={null--null},
year=2024
}

Botond Molnár, Ildikó-Beáta Márton, Szabolcs Horvát#, Mária Ercsey-Ravasz#
Community detection in directed weighted networks using Voronoi partitioning.
Sci Rep, 14(1) Art. No. 8124 (2024)
Open Access PubMed Source Full Text   

Community detection is a ubiquitous problem in applied network analysis, however efficient techniques do not yet exist for all types of network data. Directed and weighted networks are an example, where the different information encoded by link weights and the possibly high graph density can cause difficulties for some approaches. Here we present an algorithm based on Voronoi partitioning generalized to deal with directed weighted networks. As an added benefit, this method can directly employ edge weights that represent lengths, in contrast to algorithms that operate with connection strengths, requiring ad-hoc transformations of length data. We demonstrate the method on inter-areal brain connectivity, air transportation networks, and several social networks. We compare the performance with several other well-known algorithms, applying them on a set of randomly generated benchmark networks. The algorithm can handle dense graphs where weights are the main factor determining communities. The hierarchical structure of networks can also be detected, as shown for the brain. Its time efficiency is comparable or even outperforms some of the state-of-the-art algorithms, the part with the highest time-complexity being Dijkstra's shortest paths algorithm ( O(|E|+|V|log|V|) ).
@article{Molnár8715,
author={Botond Molnár, Ildikó-Beáta Márton, Szabolcs Horvát, Mária Ercsey-Ravasz},
title={Community detection in directed weighted networks using Voronoi partitioning.},
journal ={Scientific reports},
volume={14},
issue ={1},
pages={null--null},
year=2024
}

Mukesh Kumar, Canan Has, Khanh Lam-Kamath, Sophie Ayciriex, Deepshe Dewett, Mina Bashir, Clara Poupault, Kai Schuhmann, Henrik Thomas, Oskar Knittelfelder, Bharath Kumar Raghuraman, R Ahrends, Jens Rister#, Andrej Shevchenko#
Lipidome Unsaturation Affects the Morphology and Proteome of the Drosophila Eye.
J Proteome Res, 23(4) 1188-1199 (2024)
Open Access PubMed Source Full Text   

Organisms respond to dietary and environmental challenges by altering the molecular composition of their glycerolipids and glycerophospholipids (GPLs), which may favorably adjust the physicochemical properties of lipid membranes. However, how lipidome changes affect the membrane proteome and, eventually, the physiology of specific organs is an open question. We addressed this issue in Drosophila melanogaster, which is not able to synthesize sterols and polyunsaturated fatty acids but can acquire them from food. We developed a series of semisynthetic foods to manipulate the length and unsaturation of fatty acid moieties in GPLs and singled out proteins whose abundance is specifically affected by membrane lipid unsaturation in the Drosophila eye. Unexpectedly, we identified a group of proteins that have muscle-related functions and increased their abundances under unsaturated eye lipidome conditions. In contrast, the abundance of two stress response proteins, Turandot A and Smg5, is decreased by lipid unsaturation. Our findings could guide the genetic dissection of homeostatic mechanisms that maintain visual function when the eye is exposed to environmental and dietary challenges.
@article{Kumar8697,
author={Mukesh Kumar, Canan Has, Khanh Lam-Kamath, Sophie Ayciriex, Deepshe Dewett, Mina Bashir, Clara Poupault, Kai Schuhmann, Henrik Thomas, Oskar Knittelfelder, Bharath Kumar Raghuraman, R Ahrends, Jens Rister, Andrej Shevchenko},
title={Lipidome Unsaturation Affects the Morphology and Proteome of the Drosophila Eye.},
journal ={Journal of proteome research},
volume={23},
issue ={4},
pages={1188--1199},
year=2024
}

Adriano Bolondi✳︎, Benjamin K Law✳︎, Helene Kretzmer, Seher Ipek Gassaloglu, René Buschow, Christina Riemenschneider, Dian Yang, Maria Walther, Jesse V Veenvliet, Alexander Meissner#, Zachary D Smith#, Michelle M Chan#
Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids.
Dev Cell, Art. No. doi: 10.1016/j.devcel.2024.03.024 (2024)
Open Access PubMed Source   

Embryogenesis requires substantial coordination to translate genetic programs to the collective behavior of differentiating cells, but understanding how cellular decisions control tissue morphology remains conceptually and technically challenging. Here, we combine continuous Cas9-based molecular recording with a mouse embryonic stem cell-based model of the embryonic trunk to build single-cell phylogenies that describe the behavior of transient, multipotent neuro-mesodermal progenitors (NMPs) as they commit into neural and somitic cell types. We find that NMPs show subtle transcriptional signatures related to their recent differentiation and contribute to downstream lineages through a surprisingly broad distribution of individual fate outcomes. Although decision-making can be heavily influenced by environmental cues to induce morphological phenotypes, axial progenitors intrinsically mature over developmental time to favor the neural lineage. Using these data, we present an experimental and analytical framework for exploring the non-homeostatic dynamics of transient progenitor populations as they shape complex tissues during critical developmental windows.
@article{Bolondi8700,
author={Adriano Bolondi, Benjamin K Law, Helene Kretzmer, Seher Ipek Gassaloglu, René Buschow, Christina Riemenschneider, Dian Yang, Maria Walther, Jesse V Veenvliet, Alexander Meissner, Zachary D Smith, Michelle M Chan},
title={Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids.},
journal ={Developmental cell},
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, Art. No. doi: 10.1515/cclm-2023-1266 (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={},
pages={1--1},
year=2024
}

Neha Pincha Shroff✳︎, Pengfei Xu✳︎, Sangwoo Kim, Elijah R Shelton, Ben J Gross, Yucen Liu, Carlos O Gomez, Qianlin Ye, Tingsheng Yu Drennon, Jimmy K Hu, Jeremy B A Green, Otger Campàs#, Ophir D. Klein#
Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development.
Nat Cell Biol, Art. No. doi: 10.1038/s41556-024-01380-4 (2024)
PubMed Source   

Localized sources of morphogens, called signalling centres, play a fundamental role in coordinating tissue growth and cell fate specification during organogenesis. However, how these signalling centres are established in tissues during embryonic development is still unclear. Here we show that the main signalling centre orchestrating development of rodent incisors, the enamel knot (EK), is specified by a cell proliferation-driven buildup in compressive stresses (mechanical pressure) in the tissue. Direct mechanical measurements indicate that the stresses generated by cell proliferation are resisted by the surrounding tissue, creating a circular pattern of mechanical anisotropy with a region of high compressive stress at its centre that becomes the EK. Pharmacological inhibition of proliferation reduces stresses and suppresses EK formation, and application of external pressure in proliferation-inhibited conditions rescues the formation of the EK. Mechanical information is relayed intracellularly through YAP protein localization, which is cytoplasmic in the region of compressive stress that establishes the EK and nuclear in the stretched anisotropic cells that resist the pressure buildup around the EK. Together, our data identify a new role for proliferation-driven mechanical compression in the specification of a model signalling centre during mammalian organ development.
@article{Shroff8702,
author={Neha Pincha Shroff, Pengfei Xu, Sangwoo Kim, Elijah R Shelton, Ben J Gross, Yucen Liu, Carlos O Gomez, Qianlin Ye, Tingsheng Yu Drennon, Jimmy K Hu, Jeremy B A Green, Otger Campàs, Ophir D. Klein},
title={Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development.},
journal ={Nature cell biology},
volume={},
pages={1--1},
year=2024
}
✳︎ joint first authors, # joint corresponding authors
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