Sort by
Showing 21 to 30 of 2,331 entries
Show entries

Prasath Paramasivam✳︎, Christian Franke✳︎, Martin Stöter, Andreas Höijer, Stefano Bartesaghi, Alan Sabirsh, Lennart Lindfors, Marianna Yanez Arteta, Anders Dahlén, Annette Bak, Shalini Andersson, Yannis Kalaidzidis, Marc Bickle, Marino Zerial
Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale.
J Cell Biol, 221(2) Art. No. e202110137 (2022)
Open Access   PubMed Source   

Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeutics. However, a bottleneck remains in the poor understanding of the parameters that correlate with endosomal escape versus cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those used in mRNA-based vaccines, in primary human adipocytes, fibroblasts, and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery, and different LNPs vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By using super-resolution microscopy, we could resolve a single LNP-mRNA within subendosomal compartments and capture events of mRNA escape from endosomal recycling tubules. Our results change the view of the mechanisms of endosomal escape and define quantitative parameters to guide the development of mRNA formulations toward higher efficacy and lower cytotoxicity.
@article{Paramasivam8229,
author={Prasath Paramasivam, Christian Franke, Martin Stöter, Andreas Höijer, Stefano Bartesaghi, Alan Sabirsh, Lennart Lindfors, Marianna Yanez Arteta, Anders Dahlén, Annette Bak, Shalini Andersson, Yannis Kalaidzidis, Marc Bickle, Marino Zerial},
title={Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale.},
journal ={Journal of cell biology, The },
volume={221},
issue ={2},
pages={1--19},
year=2022
}

Katharina Holzhüter, Eric R Geertsma
Uniport, Not Proton-Symport, in a Non-Mammalian SLC23 Transporter.
J Mol Biol, 434(2) Art. No. 167393 (2022)
Open Access PubMed Source   

SLC23 family members are transporters of either nucleobases or ascorbate. While the mammalian SLC23 ascorbate transporters are sodium-coupled, the non-mammalian nucleobase transporters have been proposed, but not formally shown, to be proton-coupled symporters. This assignment is exclusively based on in vivo transport assays using protonophores. Here, by establishing the first in vitro transport assay for this protein family, we demonstrate that a representative member of the SLC23 nucleobase transporters operates as a uniporter instead. We explain these conflicting assignments by identifying a critical role of uracil phosphoribosyltransferase, the enzyme converting uracil to UMP, in driving uracil uptake in vivo. Detailed characterization of uracil phosphoribosyltransferase reveals that the sharp reduction of uracil uptake in whole cells in presence of protonophores is caused by acidification-induced enzyme inactivation. The SLC23 family therefore consists of both uniporters and symporters in line with the structurally related SLC4 and SLC26 families that have previously been demonstrated to accommodate both transport modes as well.
@article{Holzhüter8250,
author={Katharina Holzhüter, Eric R Geertsma},
title={Uniport, Not Proton-Symport, in a Non-Mammalian SLC23 Transporter.},
journal ={Journal of molecular biology},
volume={434},
issue ={2},
pages={null--null},
year=2022
}

Mara K N Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M Archibald, William J Baker, Katherine Belov, Mark L Blaxter, Tomas Marques Bonet, Anna K Childers, Jonathan A Coddington, Keith A Crandall, Andrew J Crawford, Robert P Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J Hoff, Kerstin Howe, Erich D Jarvis, Warren E Johnson, Rebecca N Johnson, Paul J Kersey, Xin Liu, Jose Victor Lopez, Eugene W Myers, Olga Vinnere Pettersson, Adam M Phillippy, Monica F Poelchau, Kim D Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sanjeeb Kumar Sahu, Nicholas A Salmon, Pamela S Soltis, David Swarbreck, Francoise Thibaud-Nissen, Sibo Wang, Jill L Wegrzyn, Guojie Zhang, He Zhang, Harris A Lewin, Stephen Richards
Standards recommendations for the Earth BioGenome Project.
Proc Natl Acad Sci U.S.A., 119(4) Art. No. e2115639118 (2022)
Open Access PubMed Source   

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
@article{Lawniczak8273,
author={Mara K N Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M Archibald, William J Baker, Katherine Belov, Mark L Blaxter, Tomas Marques Bonet, Anna K Childers, Jonathan A Coddington, Keith A Crandall, Andrew J Crawford, Robert P Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J Hoff, Kerstin Howe, Erich D Jarvis, Warren E Johnson, Rebecca N Johnson, Paul J Kersey, Xin Liu, Jose Victor Lopez, Eugene W Myers, Olga Vinnere Pettersson, Adam M Phillippy, Monica F Poelchau, Kim D Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sanjeeb Kumar Sahu, Nicholas A Salmon, Pamela S Soltis, David Swarbreck, Francoise Thibaud-Nissen, Sibo Wang, Jill L Wegrzyn, Guojie Zhang, He Zhang, Harris A Lewin, Stephen Richards},
title={Standards recommendations for the Earth BioGenome Project.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={119},
issue ={4},
pages={null--null},
year=2022
}

Harris A Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L Allende, John M Archibald, Miklós Bálint, Katharine B Barker, Benedikt Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L Blaxter, Jing Cai, Nicolette D Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K Childers, Jonathan A Coddington, Dalia A Conde, Montserrat Corominas, Keith A Crandall, Andrew J Crawford, Federica DiPalma, Richard Durbin, ThankGod E Ebenezer, Scott V Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A Gibbs, M Thomas P Gilbert, Melissa M Goldstein, Jennifer Marshall Graves, Henry T Greely, Ilya Grigoriev, Kevin J Hackett, Neil Hall, David Haussler, Kristofer M Helgen, Carolyn J Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D Jarvis, Warren E Johnson, Steven J. M. Jones, Elinor K Karlsson, Paul J Kersey, Jin-Hyoung Kim, W John Kress, Shigehiro Kuraku, Mara K N Lawniczak, James H Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose Victor Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A K Mazet, Camila J Mazzoni, Eugene W Myers, Rachel J O'Neill, Sadye Paez, Hyun Park, Gene E Robinson, Cristina Roquet, Oliver A Ryder, Jamal S M Sabir, H Bradley Shaffer, Timothy M Shank, Jacob S Sherkow, Pamela S Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L Wilson, Xun Xu, Huanming Yang, Anne D Yoder, Guojie Zhang
The Earth BioGenome Project 2020: Starting the clock.
Proc Natl Acad Sci U.S.A., 119(4) Art. No. e2115635118 (2022)
Open Access PubMed Source  

@article{Lewin8274,
author={Harris A Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L Allende, John M Archibald, Miklós Bálint, Katharine B Barker, Benedikt Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L Blaxter, Jing Cai, Nicolette D Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K Childers, Jonathan A Coddington, Dalia A Conde, Montserrat Corominas, Keith A Crandall, Andrew J Crawford, Federica DiPalma, Richard Durbin, ThankGod E Ebenezer, Scott V Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A Gibbs, M Thomas P Gilbert, Melissa M Goldstein, Jennifer Marshall Graves, Henry T Greely, Ilya Grigoriev, Kevin J Hackett, Neil Hall, David Haussler, Kristofer M Helgen, Carolyn J Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D Jarvis, Warren E Johnson, Steven J. M. Jones, Elinor K Karlsson, Paul J Kersey, Jin-Hyoung Kim, W John Kress, Shigehiro Kuraku, Mara K N Lawniczak, James H Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose Victor Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A K Mazet, Camila J Mazzoni, Eugene W Myers, Rachel J O'Neill, Sadye Paez, Hyun Park, Gene E Robinson, Cristina Roquet, Oliver A Ryder, Jamal S M Sabir, H Bradley Shaffer, Timothy M Shank, Jacob S Sherkow, Pamela S Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L Wilson, Xun Xu, Huanming Yang, Anne D Yoder, Guojie Zhang},
title={The Earth BioGenome Project 2020: Starting the clock.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={119},
issue ={4},
pages={null--null},
year=2022
}

David Thomas Gonzales, Naresh Yandrapalli, Tom Robinson, Christoph Zechner#, T-Y Dora Tang#
Cell-Free Gene Expression Dynamics in Synthetic Cell Populations.
ACS Synth Biol, 11(1) 205-215 (2022)
Open Access PubMed Source   

The ability to build synthetic cellular populations from the bottom-up provides the groundwork to realize minimal living tissues comprising single cells which can communicate and bridge scales into multicellular systems. Engineered systems made of synthetic micron-sized compartments and integrated reaction networks coupled with mathematical modeling can facilitate the design and construction of complex and multiscale chemical systems from the bottom-up. Toward this goal, we generated populations of monodisperse liposomes encapsulating cell-free expression systems (CFESs) using double-emulsion microfluidics and quantified transcription and translation dynamics within individual synthetic cells of the population using a fluorescent Broccoli RNA aptamer and mCherry protein reporter. CFE dynamics in bulk reactions were used to test different coarse-grained resource-limited gene expression models using model selection to obtain transcription and translation rate parameters by likelihood-based parameter estimation. The selected model was then applied to quantify cell-free gene expression dynamics in populations of synthetic cells. In combination, our experimental and theoretical approaches provide a statistically robust analysis of CFE dynamics in bulk and monodisperse synthetic cell populations. We demonstrate that compartmentalization of CFESs leads to different transcription and translation rates compared to bulk CFE and show that this is due to the semipermeable lipid membrane that allows the exchange of materials between the synthetic cells and the external environment.
@article{Gonzales8269,
author={David Thomas Gonzales, Naresh Yandrapalli, Tom Robinson, Christoph Zechner, T-Y Dora Tang},
title={Cell-Free Gene Expression Dynamics in Synthetic Cell Populations.},
journal ={ACS synthetic biology},
volume={11},
issue ={1},
pages={205--215},
year=2022
}

Jelena Krstic, Isabel Reinisch, Katharina Schindlmaier, Markus Galhuber, Zina Riahi, Natascha Berger, Nadja Kupper, Elisabeth Moyschewitz, Martina Auer, Helene Michenthaler, Christoph Nössing, Maria R Depaoli, Jeta Ramadani-Muja, Sinem Usluer, Sarah Stryeck, Martin Pichler, Beate Rinner, Alexander J A Deutsch, Andreas Reinisch, Tobias Madl, Riccardo Zenezini Chiozzi, Albert J R Heck, Meritxell Huch, Roland Malli, Andreas Prokesch
Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism.
Sci Adv, 8(3) Art. No. eabh2635 (2022)
Open Access PubMed Source   

Cancer cells voraciously consume nutrients to support their growth, exposing metabolic vulnerabilities that can be therapeutically exploited. Here, we show in hepatocellular carcinoma (HCC) cells, xenografts, and patient-derived organoids that fasting improves sorafenib efficacy and acts synergistically to sensitize sorafenib-resistant HCC. Mechanistically, sorafenib acts noncanonically as an inhibitor of mitochondrial respiration, causing resistant cells to depend on glycolysis for survival. Fasting, through reduction in glucose and impeded AKT/mTOR signaling, prevents this Warburg shift. Regulating glucose transporter and proapoptotic protein expression, p53 is necessary and sufficient for the sorafenib-sensitizing effect of fasting. p53 is also crucial for fasting-mediated improvement of sorafenib efficacy in an orthotopic HCC mouse model. Together, our data suggest fasting and sorafenib as rational combination therapy for HCC with intact p53 signaling. As HCC therapy is currently severely limited by resistance, these results should instigate clinical studies aimed at improving therapy response in advanced-stage HCC.
@article{Krstic8270,
author={Jelena Krstic, Isabel Reinisch, Katharina Schindlmaier, Markus Galhuber, Zina Riahi, Natascha Berger, Nadja Kupper, Elisabeth Moyschewitz, Martina Auer, Helene Michenthaler, Christoph Nössing, Maria R Depaoli, Jeta Ramadani-Muja, Sinem Usluer, Sarah Stryeck, Martin Pichler, Beate Rinner, Alexander J A Deutsch, Andreas Reinisch, Tobias Madl, Riccardo Zenezini Chiozzi, Albert J R Heck, Meritxell Huch, Roland Malli, Andreas Prokesch},
title={Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism.},
journal ={Science advances},
volume={8},
issue ={3},
pages={null--null},
year=2022
}

Cordula Reuther✳︎, Paula Santos-Otte✳︎, Rahul Grover, Georg Heldt, Günther Woehlke, Stefan Diez
Multiplication of Motor-Driven Microtubules for Nanotechnological Applications.
Nano Lett, Art. No. doi: 10.1021/acs.nanolett.1c03619 (2022)
PubMed Source   

Microtubules gliding on motor-functionalized surfaces have been explored for various nanotechnological applications. However, when moving over large distances (several millimeters) and long times (tens of minutes), microtubules are lost due to surface detachment. Here, we demonstrate the multiplication of kinesin-1-driven microtubules that comprises two concurrent processes: (i) severing of microtubules by the enzyme spastin and (ii) elongation of microtubules by self-assembly of tubulin dimers at the microtubule ends. We managed to balance the individual processes such that the average length of the microtubules stayed roughly constant over time while their number increased. Moreover, we show microtubule multiplication in physical networks with topographical channel structures. Our method is expected to broaden the toolbox for microtubule-based in vitro applications by counteracting the microtubule loss from substrate surfaces. Among others, this will enable upscaling of network-based biocomputation, where it is vital to increase the number of microtubules during operation.
@article{Reuther8271,
author={Cordula Reuther, Paula Santos-Otte, Rahul Grover, Georg Heldt, Günther Woehlke, Stefan Diez},
title={Multiplication of Motor-Driven Microtubules for Nanotechnological Applications.},
journal ={Nano letters},
volume={},
pages={null--null},
year=2022
}

Juliana G. Roscito#, Katrin Sameith, Bogdan Kirilenko, Nikolai Hecker, Sylke Winkler, Andreas Dahl, Miguel Trefaut Rodrigues, Michael Hiller#
Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages.
Cell Rep, 38(3) Art. No. 110280 (2022)
Open Access PubMed Source   

Loss of limbs evolved many times in squamate reptiles. Here we investigated the genomic basis of convergent limb loss in reptiles. We sequenced the genomes of a closely related pair of limbless-limbed gymnophthalmid lizards and performed a comparative genomic analysis including five snakes and the limbless glass lizard. Our analysis of these three independent limbless lineages revealed that signatures of shared sequence or transcription factor binding site divergence in individual limb regulatory elements are generally rare. Instead, shared divergence occurs more often at the level of signaling pathways, involving different regulatory elements associated with the same limb genes (such as Hand2 or Hox) and/or patterning mechanisms (such as Shh signaling). Interestingly, although snakes are known to have mutations in the Shh ZRS limb enhancer, this enhancer lacks relevant mutations in limbless lizards. Thus, different mechanisms could contribute to limb loss, and there are likely multiple evolutionary paths to limblessness in reptiles.
@article{Roscito8272,
author={Juliana G. Roscito, Katrin Sameith, Bogdan Kirilenko, Nikolai Hecker, Sylke Winkler, Andreas Dahl, Miguel Trefaut Rodrigues, Michael Hiller},
title={Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages.},
journal ={Cell reports},
volume={38},
issue ={3},
pages={null--null},
year=2022
}

German Belenguer✳︎, Gianmarco Mastrogiovanni✳︎, Clare Pacini✳︎, Zoe Hall, Anna Dowbaj, Robert Arnes-Benito, Aleksandra Sljukic, Nicole Prior, Sofia Kakava, Charles R. Bradshaw, Susan E Davies, Michele Vacca, Kourosh Saeb-Parsy, Bon-Kyoung Koo, Meritxell Huch
RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.
Nat Commun, 13(1) Art. No. 334 (2022)
Open Access PubMed Source   

RNF43/ZNRF3 negatively regulate WNT signalling. Both genes are mutated in several types of cancers, however, their contribution to liver disease is unknown. Here we describe that hepatocyte-specific loss of Rnf43/Znrf3 results in steatohepatitis and in increase in unsaturated lipids, in the absence of dietary fat supplementation. Upon injury, Rnf43/Znrf3 deletion results in defective hepatocyte regeneration and liver cancer, caused by an imbalance between differentiation/proliferation. Using hepatocyte-, hepatoblast- and ductal cell-derived organoids we demonstrate that the differentiation defects and lipid alterations are, in part, cell-autonomous. Interestingly, ZNRF3 mutant liver cancer patients present poorer prognosis, altered hepatic lipid metabolism and steatohepatitis/NASH signatures. Our results imply that RNF43/ZNRF3 predispose to liver cancer by controlling the proliferative/differentiation and lipid metabolic state of hepatocytes. Both mechanisms combined facilitate the progression towards malignancy. Our findings might aid on the management of those RNF43/ZNRF3 mutated individuals at risk of developing fatty liver and/or liver cancer.
@article{Belenguer8268,
author={German Belenguer, Gianmarco Mastrogiovanni, Clare Pacini, Zoe Hall, Anna Dowbaj, Robert Arnes-Benito, Aleksandra Sljukic, Nicole Prior, Sofia Kakava, Charles R. Bradshaw, Susan E Davies, Michele Vacca, Kourosh Saeb-Parsy, Bon-Kyoung Koo, Meritxell Huch},
title={RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.},
journal ={Nature communications},
volume={13},
issue ={1},
pages={null--null},
year=2022
}

Bharath Kumar Raghuraman, Aliona Bogdanova, HongKee Moon, Ignacy Rzagalinski, Eric R Geertsma, Lena Hersemann, Andrej Shevchenko
Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS).
J Proteome Res, 21(1) 132-141 (2022)
Open Access PubMed Source   

By reporting the molar abundance of proteins, absolute quantification determines their stoichiometry in complexes, pathways, or networks. Typically, absolute quantification relies either on protein-specific isotopically labeled peptide standards or on a semiempirical calibration against the average abundance of peptides chosen from arbitrarily selected proteins. In contrast, a generic protein standard FUGIS (fully unlabeled generic internal standard) requires no isotopic labeling, chemical synthesis, or external calibration and is applicable to quantifying proteins of any organismal origin. The median intensity of the peptide peaks produced by the tryptic digestion of FUGIS is used as a single-point calibrant to determine the molar abundance of any codigested protein. Powered by FUGIS, median-based absolute quantification (MBAQ) outperformed other methods of untargeted proteome-wide absolute quantification.
@article{Raghuraman8215,
author={Bharath Kumar Raghuraman, Aliona Bogdanova, HongKee Moon, Ignacy Rzagalinski, Eric R Geertsma, Lena Hersemann, Andrej Shevchenko},
title={Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS).},
journal ={Journal of proteome research},
volume={21},
issue ={1},
pages={132--141},
year=2022
}


✳︎ joined first author, # joined corresponding author
--%>