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Fereshteh R Najafabadi✳︎, Mark Leaver✳︎, Stephan W. Grill
Orchestrating nonmuscle myosin II filament assembly at the onset of cytokinesis.
Mol Biol Cell, 33(8) Art. No. ar74 (2022)
PubMed Source   

Contractile forces in the actomyosin cortex are required for cellular morphogenesis. This includes the invagination of the cell membrane during division, where filaments of nonmuscle myosin II (NMII) are responsible for generating contractile forces in the cortex. However, how NMII heterohexamers form filaments in vivo is not well understood. To quantify NMII filament assembly dynamics, we imaged the cortex of Caenorhabditis elegans embryos at high spatial resolution around the time of the first division. We show that during the assembly of the cytokinetic ring, the number of NMII filaments in the cortex increases and more NMII motors are assembled into each filament. These dynamics are influenced by two proteins in the RhoA GTPase pathway, the RhoA-dependent kinase LET-502 and the myosin phosphatase MEL-11. We find that these two proteins differentially regulate NMII activity at the anterior and at the division site. We show that the coordinated action of these regulators generates a gradient of free NMII in the cytoplasm driving a net diffusive flux of NMII motors toward the cytokinetic ring. Our work highlights how NMII filament assembly and disassembly dynamics are orchestrated over space and time to facilitate the up-regulation of cortical contractility during cytokinesis.
@article{Najafabadi8351,
author={Fereshteh R Najafabadi, Mark Leaver, Stephan W. Grill},
title={Orchestrating nonmuscle myosin II filament assembly at the onset of cytokinesis.},
journal ={Molecular biology of the cell},
volume={33},
issue ={8},
pages={null--null},
year=2022
}

Aleksandra Spiegel, Chris Lauber, Mandy Bachmann, Anne-Kristin Heninger, Christian Klose, Kai Simons, Mihail Sarov, Mathias J. Gerl
A set of gene knockouts as a resource for global lipidomic changes.
Sci Rep, 12(1) Art. No. 10533 (2022)
Open Access PubMed Source   

Enzyme specificity in lipid metabolic pathways often remains unresolved at the lipid species level, which is needed to link lipidomic molecular phenotypes with their protein counterparts to construct functional pathway maps. We created lipidomic profiles of 23 gene knockouts in a proof-of-concept study based on a CRISPR/Cas9 knockout screen in mammalian cells. This results in a lipidomic resource across 24 lipid classes. We highlight lipid species phenotypes of multiple knockout cell lines compared to a control, created by targeting the human safe-harbor locus AAVS1 using up to 1228 lipid species and subspecies, charting lipid metabolism at the molecular level. Lipid species changes are found in all knockout cell lines, however, some are most apparent on the lipid class level (e.g., SGMS1 and CEPT1), while others are most apparent on the fatty acid level (e.g., DECR2 and ACOT7). We find lipidomic phenotypes to be reproducible across different clones of the same knockout and we observed similar phenotypes when two enzymes that catalyze subsequent steps of the long-chain fatty acid elongation cycle were targeted.
@article{Spiegel8384,
author={Aleksandra Spiegel, Chris Lauber, Mandy Bachmann, Anne-Kristin Heninger, Christian Klose, Kai Simons, Mihail Sarov, Mathias J. Gerl},
title={A set of gene knockouts as a resource for global lipidomic changes.},
journal ={Scientific reports},
volume={12},
issue ={1},
pages={null--null},
year=2022
}

Henrike Indrischek, John A Hammer, Anja Machate, Nikolai Hecker, Bogdan Kirilenko, Juliana G. Roscito, Stefan Hans, Caren Norden, Michael Brand#, Michael Hiller#
Vision-related convergent gene losses reveal SERPINE3's unknown role in the eye.
Elife, 11 Art. No. e77999 (2022)
Open Access PubMed Source   

Despite decades of research, knowledge about the genes that are important for development and function of the mammalian eye and are involved in human eye disorders remains incomplete. During mammalian evolution, mammals that naturally exhibit poor vision or regressive eye phenotypes have independently lost many eye-related genes. This provides an opportunity to predict novel eye-related genes based on specific evolutionary gene loss signatures. Building on these observations, we performed a genome-wide screen across 49 mammals for functionally uncharacterized genes that are preferentially lost in species exhibiting lower visual acuity values. The screen uncovered several genes, including SERPINE3, a putative serine proteinase inhibitor. A detailed investigation of 381 additional mammals revealed that SERPINE3 is independently lost in 18 lineages that typically do not primarily rely on vision, predicting a vision-related function for this gene. To test this, we show that SERPINE3 has the highest expression in eyes of zebrafish and mouse. In the zebrafish retina, serpine3 is expressed in Müller glia cells, a cell type essential for survival and maintenance of the retina. A CRISPR-mediated knockout of serpine3 in zebrafish resulted in alterations in eye shape and defects in retinal layering. Furthermore, two human polymorphisms that are in linkage with SERPINE3 are associated with eye-related traits. Together, these results suggest that SERPINE3 has a role in vertebrate eyes. More generally, by integrating comparative genomics with experiments in model organisms, we show that screens for specific phenotype-associated gene signatures can predict functions of uncharacterized genes.
@article{Indrischek8383,
author={Henrike Indrischek, John A Hammer, Anja Machate, Nikolai Hecker, Bogdan Kirilenko, Juliana G. Roscito, Stefan Hans, Caren Norden, Michael Brand, Michael Hiller},
title={Vision-related convergent gene losses reveal SERPINE3's unknown role in the eye.},
journal ={eLife},
volume={11},
pages={null--null},
year=2022
}

Suryanarayana Maddu, Bevan Cheeseman, Ivo F. Sbalzarini, Christian L. Müller
Stability selection enables robust learning of differential equations from limited noisy data
Proc. R. Soc. A, 478(2262) Art. No. 20210916 (2022)
Open Access   Source   

We present a statistical learning framework for robust identification of differential equations from noisy spatio-temporal data. We address two issues that have so far limited the application of such methods, namely their robustness against noise and the need for manual parameter tuning, by proposing stability- based model selection to determine the level of regularization required for reproducible inference. This avoids manual parameter tuning and improves robustness against noise in the data. Our stability selection approach, termed PDE-STRIDE, can be combined with any sparsity-promoting regression method and provides an interpretable criterion for model component importance. We show that the particular combination of stability selection with the iterative hard-thresholding algorithm from compressed sensing provides a fast and robust framework for equation inference that outperforms previous approaches with respect to accuracy, amount of data required, and robustness. We illustrate the performance of PDE-STRIDE on a range of simulated benchmark problems, and we 2 demonstrate the applicability of PDE-STRIDE on real-world data by considering purely data-driven inference of the protein interaction network for embryonic polarization in Caenorhabditis elegans. Using fluorescence microscopy images of C. elegans zygotes as input data, PDE-STRIDE is able to learn the molecular interactions of the proteins.
@article{Maddu8372,
author={Suryanarayana Maddu, Bevan Cheeseman, Ivo F. Sbalzarini, Christian L. Müller},
title={Stability selection enables robust learning of differential equations from limited noisy data},
journal ={Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
volume={478},
issue ={2262},
pages={1--25},
year=2022
}

Joel Jonsson, Bevan Cheeseman, Suryanarayana Maddu, Krzysztof Gonciarz, Ivo F. Sbalzarini
Parallel Discrete Convolutions on Adaptive Particle Representations of Images.
IEEE Trans Image Process, 31 4197-4212 (2022)
Open Access   PubMed Source   

We present data structures and algorithms for native implementations of discrete convolution operators over Adaptive Particle Representations (APR) of images on parallel computer architectures. The APR is a content-adaptive image representation that locally adapts the sampling resolution to the image signal. It has been developed as an alternative to pixel representations for large, sparse images as they typically occur in fluorescence microscopy. It has been shown to reduce the memory and runtime costs of storing, visualizing, and processing such images. This, however, requires that image processing natively operates on APRs, without intermediately reverting to pixels. Designing efficient and scalable APR-native image processing primitives, however, is complicated by the APR's irregular memory structure. Here, we provide the algorithmic building blocks required to efficiently and natively process APR images using a wide range of algorithms that can be formulated in terms of discrete convolutions. We show that APR convolution naturally leads to scale-adaptive algorithms that efficiently parallelize on multi-core CPU and GPU architectures. We quantify the speedups in comparison to pixel-based algorithms and convolutions on evenly sampled data. We achieve pixel-equivalent throughputs of up to 1TB/s on a single Nvidia GeForce RTX 2080 gaming GPU, requiring up to two orders of magnitude less memory than a pixel-based implementation.
@article{Jonsson8374,
author={Joel Jonsson, Bevan Cheeseman, Suryanarayana Maddu, Krzysztof Gonciarz, Ivo F. Sbalzarini},
title={Parallel Discrete Convolutions on Adaptive Particle Representations of Images.},
journal ={IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},
volume={31},
pages={4197--4212},
year=2022
}

Mark Leaver, Eduardo Moreno, Merve Kayhan, Angela McGaughran, Christian Rödelsperger, Ralf J Sommer, Anthony Hyman
Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus.
Evolution, Art. No. doi: 10.1111/evo.14520 (2022)
Open Access PubMed Source   

Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of P. pacificus at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. Together, these data indicate that P. pacificus strains on La Réunion are subject to divergent selection, adapting to hot and cold niches at the coast and summit of the volcano. Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations. This article is protected by copyright. All rights reserved.
@article{Leaver8375,
author={Mark Leaver, Eduardo Moreno, Merve Kayhan, Angela McGaughran, Christian Rödelsperger, Ralf J Sommer, Anthony Hyman},
title={Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus.},
journal ={Evolution; international journal of organic evolution},
volume={},
pages={null--null},
year=2022
}

Berna Sozen#, Deniz Conkar, Jesse V Veenvliet#
Carnegie in 4D? Stem-cell-based models of human embryo development.
Semin Cell Dev Biol, Art. No. doi: 10.1016/j.semcdb.2022.05.023 (2022)
PubMed Source   

How cells build embryos is still a major mystery. Many unresolved questions require the study of the processes that pattern and shape the embryo in live specimens, in toto, across spatial and temporal scales. In mammalian embryogenesis, this remains a major challenge as the embryo develops in utero, precluding easy accessibility. For human embryos, technical, ethical and legal limitations further hamper the in-depth investigation of embryogenesis, especially beyond gastrulation stages. This has resulted in an over-reliance on model organisms, particularly mice, to understand mammalian development. However, recent efforts show critical differences between rodent and primate embryos, including timing, architecture and transcriptional regulation. Thus, a human-centric understanding of embryogenesis is much needed. To empower this, novel in vitro approaches, which coax human pluripotent stem cells to form embryonic organoids that model embryo development, are pivotal. Here, we summarize these emergent technologies that recapitulate aspects of human development "in a dish". We show how these technologies can provide insights into the molecular, cellular and morphogenetic processes that fuel the formation of a fully formed fetus, and discuss the potential of these platforms to revolutionize our understanding of human development in health and disease. Despite their clear promise, we caution against over-interpreting the extent to which these in vitro platforms model the natural embryo. In particular, we discuss how fate, form and function - a tightly coupled trinity in vivo, can be disconnected in vitro. Finally, we propose how careful benchmarking of existing models, in combination with rational protocol design based on an increased understanding of in vivo developmental dynamics and insights from mouse in vitro models of embryo development, will help guide the establishment of better models of human embryo development.
@article{Sozen8377,
author={Berna Sozen, Deniz Conkar, Jesse V Veenvliet},
title={Carnegie in 4D? Stem-cell-based models of human embryo development.},
journal ={Seminars in cell & developmental biology},
volume={},
pages={null--null},
year=2022
}

Daxiao Sun, Isabel LuValle-Burke, Karina Pombo-García, Alf Honigmann
Biomolecular condensates in epithelial junctions.
Curr Opin Cell Biol, 77 Art. No. 102089 (2022)
PubMed Source   

Epithelial junctions are transmembrane protein complexes that regulate cell adhesion, cell polarity, tissue permeability, and tissue mechanics. Most junctional complexes contain membrane attached cytoplasmic plaques that regulate junction assembly and are composed of multivalent scaffold proteins. In this review, we discuss phase separation of multivalent proteins as a general process that drives assembly of many membrane-less cellular compartments. And we summarise recent evidence that phase separation of junctional scaffold proteins is involved in the assembly of tight junctions and focal adhesions.
@article{Sun8376,
author={Daxiao Sun, Isabel LuValle-Burke, Karina Pombo-García, Alf Honigmann},
title={Biomolecular condensates in epithelial junctions.},
journal ={Current opinion in cell biology},
volume={77},
pages={null--null},
year=2022
}

Eleonora Patsenker, Veera Raghavan Thangapandi, Oskar Knittelfelder, Alessandra Palladini, Michaela Hefti, Jane Beil-Wagner, Gerhard Rogler, Thorsten Buch, Andrej Shevchenko, Jochen Hampe, Felix Stickel
The Pnpla3 Variant I148M Reveals Protective Effects Towards Hepatocellular Carcinoma in Mice via Restoration of Omega-3 Polyunsaturated Fats.
J Nutr Biochem, Art. No. doi: 10.1016/j.jnutbio.2022.109081 (2022)
PubMed Source   

Alcohol consumption and high caloric diet are leading causes of progressive fatty liver disease. Genetic variant rs738409 in patatin-like phospholipase domain-containing protein 3 (PNPLA3 rs738409 C>G) has been repeatedly described as one of the major risk loci for alcoholic liver cirrhosis (ALC) and hepatocellular carcinoma (HCC) in humans, however, the mechanism behind this association is incompletely understood. We generated mice carrying the rs738409 variant (PNPLA3 I148M) in order to detect genotype-phenotype relationships in mice upon chow and alcohol-high fat/high sugar diet (EtOH/WD). We could clearly demonstrate that the presence of rs738409 per se is sufficient to induce spontaneous development of steatosis after one year in mice on a chow diet, whereas in the setting of unhealthy diet feeding, PNPLA3 I148M did not affect hepatic inflammation or fibrosis, but induced a striking lipid remodelling, microvesicular steatosis and protected from HCC formation. Using shot gun lipidomics, we detected a striking restoration of reduced long chain-polyunsaturated fatty acids (LC-PUFA)-containing TGs, docosapentaenoic acid (C22:5 n3) and omega-3-derived eicosanoids (5-HEPE, 20-HEPE, 19,20-EDP, 21-HDHA) in PNPLA3 I148M mice upon EtOH/WD. At the molecular level, PNPLA3 I148M modulated enzymes for fatty acid and TG transport and metabolism. These findings suggest (dietary) lipids as an important and independent driver of hepatic tumorigenesis. Genetic variant in PNPLA3 exerted protective effects in mice, conflicting with findings in humans. Species-related differences in physiology and metabolism should be taken into account when modelling unhealthy human lifestyle, as genetic mouse models may not always allow for translation of insight gained in humans.
@article{Patsenker8369,
author={Eleonora Patsenker, Veera Raghavan Thangapandi, Oskar Knittelfelder, Alessandra Palladini, Michaela Hefti, Jane Beil-Wagner, Gerhard Rogler, Thorsten Buch, Andrej Shevchenko, Jochen Hampe, Felix Stickel},
title={The Pnpla3 Variant I148M Reveals Protective Effects Towards Hepatocellular Carcinoma in Mice via Restoration of Omega-3 Polyunsaturated Fats.},
journal ={The Journal of nutritional biochemistry},
volume={},
pages={null--null},
year=2022
}

Ignacy Rzagalinski, Aliona Bogdanova, Bharath Kumar Raghuraman, Eric R Geertsma, Lena Hersemann, Tjalf Ziemssen, Andrej Shevchenko
FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards.
J Proteome Res, 21(6) 1408-1417 (2022)
Open Access PubMed Source   

Absolute (molar) quantification of clinically relevant proteins determines their reference values in liquid and solid biopsies. The FastCAT (for Fast-track QconCAT) method employs multiple short (<50 kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated quantotypic (Q)-peptides representing the quantified proteins. Each CP also comprises scrambled sequences of reference (R)-peptides that relate its abundance to a single protein standard (bovine serum albumin, BSA). FastCAT not only alleviates the need to purify CP or use sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but also improves the accuracy, precision, and dynamic range of the absolute quantification by grouping Q-peptides according to the expected abundance of the target proteins. We benchmarked FastCAT against the reference method of MS Western and tested it in the direct molar quantification of neurological markers in human cerebrospinal fluid at the low ng/mL level.
@article{Rzagalinski8349,
author={Ignacy Rzagalinski, Aliona Bogdanova, Bharath Kumar Raghuraman, Eric R Geertsma, Lena Hersemann, Tjalf Ziemssen, Andrej Shevchenko},
title={FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards.},
journal ={Journal of proteome research},
volume={21},
issue ={6},
pages={1408--1417},
year=2022
}


✳︎ joined first author, # joined corresponding author
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