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Denis Corbeil, Wieland B. Huttner
Protein tyrosine sulfation.
In: Encyclopedia of Biological Chemistry 3rd Edition. (Eds.) Joseph Jez,Amsterdam, Netherlands,Elsevier (2021),1-14
Full Text  

Sarita Hebbar, Elisabeth Knust
Reactive oxygen species (ROS) constitute an additional player in regulating epithelial development.
Bioessays, Art. No. 2100096 (2021)
PubMed Source   

Reactive oxygen species (ROS) are highly reactive molecules produced in cells. So far, they have mostly been connected to diseases and pathological conditions. More recent results revealed a somewhat unexpected role of ROS in control of developmental processes. In this review, we elaborate on ROS in development, focussing on their connection to epithelial tissue morphogenesis. After briefly summarising unique characteristics of epithelial cells, we present some characteristic features of ROS species, their production and targets, with a focus on proteins important for epithelial development and function. Finally, we provide examples of regulation of epithelial morphogenesis by ROS, and also of developmental genes that regulate the overall redox status. We conclude by discussing future avenues of research that will further elucidate ROS regulation in epithelial development.
@article{Hebbar8111,
author={Sarita Hebbar, Elisabeth Knust},
title={Reactive oxygen species (ROS) constitute an additional player in regulating epithelial development.},
journal ={BioEssays : news and reviews in molecular, cellular and developmental biology},
volume={},
pages={null--null},
year=2021
}

Leilei Xu, Mahboob Ali, Wenxiu Duan, Xiao Yuan#, Fatima Garba, McKay Mullen, Binwen Sun, Ina Poser, Hequan Duan, Jianlin Lu, Ruijun Tian, Yushu Ge, Lingluo Chu, Weijun Pan, Dongmei Wang, Anthony Hyman, Hadiyah Green, Lin Li, Zhen Dou#, Dan Liu#, Xing Liu#, Xuebiao Yao#
Feedback control of PLK1 by Apolo1 ensures accurate chromosome segregation.
Cell Rep, 36(2) Art. No. 109343 (2021)
Open Access PubMed Source   

Stable transmission of genetic material during cell division requires accurate chromosome segregation. PLK1 dynamics at kinetochores control establishment of correct kinetochore-microtubule attachments and subsequent silencing of the spindle checkpoint. However, the regulatory mechanism responsible for PLK1 activity in prometaphase has not yet been affirmatively identified. Here we identify Apolo1, which tunes PLK1 activity for accurate kinetochore-microtubule attachments. Apolo1 localizes to kinetochores during early mitosis, and suppression of Apolo1 results in misaligned chromosomes. Using the fluorescence resonance energy transfer (FRET)-based PLK1 activity reporter, we found that Apolo1 sustains PLK1 kinase activity at kinetochores for accurate attachment during prometaphase. Apolo1 is a cognate substrate of PLK1, and the phosphorylation enables PP1γ to inactivate PLK1 by dephosphorylation. Mechanistically, Apolo1 constitutes a bridge between kinase and phosphatase, which governs PLK1 activity in prometaphase. These findings define a previously uncharacterized feedback loop by which Apolo1 provides fine-tuning for PLK1 to guide chromosome segregation in mitosis.
@article{Xu8112,
author={Leilei Xu, Mahboob Ali, Wenxiu Duan, Xiao Yuan, Fatima Garba, McKay Mullen, Binwen Sun, Ina Poser, Hequan Duan, Jianlin Lu, Ruijun Tian, Yushu Ge, Lingluo Chu, Weijun Pan, Dongmei Wang, Anthony Hyman, Hadiyah Green, Lin Li, Zhen Dou, Dan Liu, Xing Liu, Xuebiao Yao},
title={Feedback control of PLK1 by Apolo1 ensures accurate chromosome segregation.},
journal ={Cell reports},
volume={36},
issue ={2},
pages={null--null},
year=2021
}

Sarah Fischer, Rohan Jain#, Thomas Krause, Purvi Jain, Satoru Tsushima, Anna Shevchenko, René Hübner, Norbert Jordan#
Impact of the Microbial Origin and Active Microenvironment on the Shape of Biogenic Elemental Selenium Nanomaterials.
Environ Sci Technol, 55(13) 9161-9171 (2021)
PubMed Source   

The shape of nanomaterials affects their colloidal properties, cellular uptake, and fate in the environment. The microbial origin and microenvironment can play a role in altering the shape of the nanomaterial. However, such studies have never been conducted. Here, we demonstrate that the selenium nanomaterials produced by Escherichia coli K-12 are stable and remain as BioSe-Nanospheres under thermophilic conditions, while those produced by anaerobic granular sludge transform to BioSe-Nanorods, due to a lower quantity of proteins coating these nanoparticles, which has been verified by proteomics analysis as well as using chemically synthesized selenium nanomaterials. Furthermore, the presence of Bacillus safensis JG-B5T transform the purified BioSe-Nanospheres produced by E. coli K-12 to BioSe-Nanorods, though they are not transformed in the absence of B. safensis JG-B5T. This is due to the production of peptidases by B. safensis JG-B5T that cleaves the protein coating the BioSe-Nanospheres produced by E. coli K-12, leading to their transformation to trigonal BioSe-Nanorods, which is the thermodynamically more stable state. These findings suggest that the fate of selenium and probably other redox-active elements released from the biological wastewater treatment units needs to be reevaluated and improved by including microbial criteria for better accuracy.
@article{Fischer8058,
author={Sarah Fischer, Rohan Jain, Thomas Krause, Purvi Jain, Satoru Tsushima, Anna Shevchenko, René Hübner, Norbert Jordan},
title={Impact of the Microbial Origin and Active Microenvironment on the Shape of Biogenic Elemental Selenium Nanomaterials.},
journal ={Environmental science & technology},
volume={55},
issue ={13},
pages={9161--9171},
year=2021
}

Pietro Incardona, Tommaso Bianucci, Ivo F. Sbalzarini
Distributed Sparse Block Grids on GPUs.
In: High Performance Computing : 36th International Conference, ISC High Performance 2021, Virtual Event, June 24 – July 2, 2021, Proceedings (2021) Lecture Notes in Computer Science ; 12728, Cham, Springer International Publishing (2021), 272-290
Source   

We present a design and implementation of distributed sparse block grids that transparently scale from a single CPU to multi-GPU clusters. We support dynamic sparse grids as, e.g., occur in computer graphics with complex deforming geometries and in multi-resolution numerical simulations. We present the data structures and algorithms of our approach, focusing on the optimizations required to render them computationally efficient on CPUs and GPUs alike. We provide a scalable implementation in the OpenFPM software library for HPC. We benchmark our implementation on up to 16 Nvidia GTX 1080 GPUs and up to 64 Nvidia A100 GPUs showing state-of-the-art scalability (68% to 96% parallel efficiency) on three benchmark problems. On a single GPU, our implementation is 14 to 140-fold faster than on a multi-core CPU.
@proceedings{Incardona8080,
title = {Distributed Sparse Block Grids on GPUs.},
year = 2021,
editor = {Pietro Incardona, Tommaso Bianucci, Ivo F. Sbalzarini},
volume = {High Performance Computing : 36th International Conference, ISC High Performance 2021, Virtual Event, June 24 – July 2, 2021, Proceedings },
series = {Lecture Notes in Computer Science ; 12728},
publisher = {Springer International Publishing}
}

Glyn Nelson✳︎#, Ulrike Boehm✳︎#, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M Brown, Aurélien Dauphin, Ian M Dobbie, John E Eriksson, Orestis Faklaris, Julia Fernandez-Rodriguez, Alexia Ferrand, Laurent Gelman, Ali Gheisari, Hella Hartmann, Christian Kukat, Alex Laude, Miso Mitkovski, Sebastian Munck, Alison J North, Tobias Manuel Rasse, Ute Resch-Genger, Lucas C Schuetz, Arne Seitz, Caterina Strambio-De-Castillia, Jason R Swedlow, Ioannis Alexopoulos, Karin Aumayr, Sergiy Avilov, Gert-Jan Bakker, Rodrigo R Bammann, Andrea Bassi, Hannes Beckert, Sebastian Beer, Yury Belyaev, Jakob Bierwagen, Konstantin A Birngruber, Manel Bosch, Juergen Breitlow, Lisa A Cameron, Joe Chalfoun, James J Chambers, Chieh-Li Chen, Eduardo Conde-Sousa, Alexander D Corbett, Fabrice P Cordelieres, Elaine Del Nery, Ralf Dietzel, Frank Eismann, Elnaz Fazeli, Andreas Felscher, Hans-Ulrich Fried, Nathalie Gaudreault, Wah Ing Goh, Thomas Guilbert, Roland Hadleigh, Peter Hemmerich, Gerhard A Holst, Michelle S Itano, Claudia B Jaffe, Helena Jambor, Stuart C Jarvis, Antje Keppler, David Kirchenbuechler, Marcel Kirchner, Norio Kobayashi, Gabriel Krens, Susanne Kunis, Judith Lacoste, Maresca Marcello, Gabriel G Martins, Daniel J Metcalf, Claire A Mitchell, Joshua Moore, Tobias Mueller, Michael S Nelson, Stephen Ogg, Shuichi Onami, Alexandra L Palmer, Perrine Paul-Gilloteaux, Jaime A Pimentel, Laure Plantard, Santosh Podder, Elton Rexhepaj, Arnaud Royon, Markku A Saari, Damien Schapman, Vincent Schoonderwoert, Britta Schroth-Diez, Stanley Schwartz, Michael Shaw, Martin Spitaler, Martin T Stoeckl, Damir Sudar, Jeremie Teillon, Stefan Terjung, Roland Thuenauer, Christian D Wilms, Graham D Wright, Roland Nitschke#
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.
J Microsc, Art. No. 10.1111/jmi.13041 (2021)
PubMed Source   

A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated, quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments1 . One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique2,3 . Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g., DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE4 ), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility5 . In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative6 was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models7,8 , and tools9,10 , including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists11 , bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
@article{Nelson8102,
author={Glyn Nelson, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M Brown, Aurélien Dauphin, Ian M Dobbie, John E Eriksson, Orestis Faklaris, Julia Fernandez-Rodriguez, Alexia Ferrand, Laurent Gelman, Ali Gheisari, Hella Hartmann, Christian Kukat, Alex Laude, Miso Mitkovski, Sebastian Munck, Alison J North, Tobias Manuel Rasse, Ute Resch-Genger, Lucas C Schuetz, Arne Seitz, Caterina Strambio-De-Castillia, Jason R Swedlow, Ioannis Alexopoulos, Karin Aumayr, Sergiy Avilov, Gert-Jan Bakker, Rodrigo R Bammann, Andrea Bassi, Hannes Beckert, Sebastian Beer, Yury Belyaev, Jakob Bierwagen, Konstantin A Birngruber, Manel Bosch, Juergen Breitlow, Lisa A Cameron, Joe Chalfoun, James J Chambers, Chieh-Li Chen, Eduardo Conde-Sousa, Alexander D Corbett, Fabrice P Cordelieres, Elaine Del Nery, Ralf Dietzel, Frank Eismann, Elnaz Fazeli, Andreas Felscher, Hans-Ulrich Fried, Nathalie Gaudreault, Wah Ing Goh, Thomas Guilbert, Roland Hadleigh, Peter Hemmerich, Gerhard A Holst, Michelle S Itano, Claudia B Jaffe, Helena Jambor, Stuart C Jarvis, Antje Keppler, David Kirchenbuechler, Marcel Kirchner, Norio Kobayashi, Gabriel Krens, Susanne Kunis, Judith Lacoste, Maresca Marcello, Gabriel G Martins, Daniel J Metcalf, Claire A Mitchell, Joshua Moore, Tobias Mueller, Michael S Nelson, Stephen Ogg, Shuichi Onami, Alexandra L Palmer, Perrine Paul-Gilloteaux, Jaime A Pimentel, Laure Plantard, Santosh Podder, Elton Rexhepaj, Arnaud Royon, Markku A Saari, Damien Schapman, Vincent Schoonderwoert, Britta Schroth-Diez, Stanley Schwartz, Michael Shaw, Martin Spitaler, Martin T Stoeckl, Damir Sudar, Jeremie Teillon, Stefan Terjung, Roland Thuenauer, Christian D Wilms, Graham D Wright, Roland Nitschke},
title={QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.},
journal ={Journal of microscopy},
volume={},
pages={null--null},
year=2021
}

Chang-Yu Chang✳︎, Jean C C Vila✳︎, Madeline Bender, Richard Li, Madeleine C Mankowski, Molly Bassette, Julia Borden, Stefan Golfier, Paul Gerald L Sanchez, Rachel Waymack, Xinwen Zhu, Juan Diaz-Colunga, Sylvie Estrela, Maria Rebolleda-Gomez, Alvaro Sanchez
Engineering complex communities by directed evolution.
Nat Ecol Evol, 5(7) 1011-1023 (2021)
PubMed Source   

Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.
@article{Chang8079,
author={Chang-Yu Chang, Jean C C Vila, Madeline Bender, Richard Li, Madeleine C Mankowski, Molly Bassette, Julia Borden, Stefan Golfier, Paul Gerald L Sanchez, Rachel Waymack, Xinwen Zhu, Juan Diaz-Colunga, Sylvie Estrela, Maria Rebolleda-Gomez, Alvaro Sanchez},
title={Engineering complex communities by directed evolution.},
journal ={Nature ecology & evolution},
volume={5},
issue ={7},
pages={1011--1023},
year=2021
}

Lei Xing, Agnieszka Kubik-Zahorodna, Takashi Namba, Anneline Pinson, Marta Florio, Jan Prochazka, Mihail Sarov, Radislav Sedlacek, Wieland Huttner
Expression of human-specific ARHGAP11B in mice leads to neocortex expansion and increased memory flexibility.
EMBO J, 40(13) Art. No. 107093 (2021)
Open Access PubMed Source   

Neocortex expansion during human evolution provides a basis for our enhanced cognitive abilities. Yet, which genes implicated in neocortex expansion are actually responsible for higher cognitive abilities is unknown. The expression of human-specific ARHGAP11B in embryonic/foetal mouse, ferret and marmoset neocortex was previously found to promote basal progenitor proliferation, upper-layer neuron generation and neocortex expansion during development, features commonly thought to contribute to increased cognitive abilities. However, a key question is whether this phenotype persists into adulthood and if so, whether cognitive abilities are indeed increased. Here, we generated a transgenic mouse line with physiological ARHGAP11B expression that exhibits increased neocortical size and upper-layer neuron numbers persisting into adulthood. Adult ARHGAP11B-transgenic mice showed altered neurobehaviour, notably increased memory flexibility and a reduced anxiety level. Our data are consistent with the notion that neocortex expansion by ARHGAP11B, a gene implicated in human evolution, underlies some of the altered neurobehavioural features observed in the transgenic mice, such as the increased memory flexibility, a neocortex-associated trait, with implications for the increase in cognitive abilities during human evolution.
@article{Xing8043,
author={Lei Xing, Agnieszka Kubik-Zahorodna, Takashi Namba, Anneline Pinson, Marta Florio, Jan Prochazka, Mihail Sarov, Radislav Sedlacek, Wieland Huttner},
title={Expression of human-specific ARHGAP11B in mice leads to neocortex expansion and increased memory flexibility.},
journal ={The EMBO journal},
volume={40},
issue ={13},
pages={null--null},
year=2021
}

Emiel P C van der Vorst✳︎#, Mario A A Pepe✳︎, Linsey J F Peters, Markus Haberbosch, Yvonne Jansen, Ronald Naumann, Georgios T Stathopoulos, Christian Weber, Kiril Bidzhekov#
Transcriptome signature of miRNA-26b KO mouse model suggests novel targets.
BMC Genom Data, 22(1) Art. No. 23 (2021)
Open Access PubMed Source   

MicroRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. One of the miRNAs that has been shown to play a role in various pathologies like cancer, neurological disorders and cardiovascular diseases is miRNA-26b. However, these studies only demonstrated rather ambiguous associations without revealing a causal relationship. Therefore, the aim of this study is to establish and validate a mouse model which enables the elucidation of the exact role of miRNA-26b in various pathologies.
@article{Vorst8114,
author={Emiel P C van der Vorst, Mario A A Pepe, Linsey J F Peters, Markus Haberbosch, Yvonne Jansen, Ronald Naumann, Georgios T Stathopoulos, Christian Weber, Kiril Bidzhekov},
title={Transcriptome signature of miRNA-26b KO mouse model suggests novel targets.},
journal ={BMC genomic data},
volume={22},
issue ={1},
pages={null--null},
year=2021
}

Xingbo Yang✳︎#, Matthias Heinemann, Jonathon Howard, Greg Huber, Srividya Iyer-Biswas, Guillaume Le Treut, Michael Lynch, Kristi L Montooth, Daniel Needleman, Simone Pigolotti, Jonathan Rodenfels, Pierre Ronceray, Sadasivan Shankar, Iman Tavassoly, Shashi Thutupalli, Denis V Titov, Jin Wang, Peter J Foster✳︎#
Physical bioenergetics: Energy fluxes, budgets, and constraints in cells.
Proc Natl Acad Sci U.S.A., 118(26) Art. No. e2026786118 (2021)
PubMed Source   

Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. Here we review recent advances and discuss open questions and challenges in physical bioenergetics.
@article{Yang8088,
author={Xingbo Yang, Matthias Heinemann, Jonathon Howard, Greg Huber, Srividya Iyer-Biswas, Guillaume Le Treut, Michael Lynch, Kristi L Montooth, Daniel Needleman, Simone Pigolotti, Jonathan Rodenfels, Pierre Ronceray, Sadasivan Shankar, Iman Tavassoly, Shashi Thutupalli, Denis V Titov, Jin Wang, Peter J Foster},
title={Physical bioenergetics: Energy fluxes, budgets, and constraints in cells.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={118},
issue ={26},
pages={null--null},
year=2021
}


✳︎ joined first author, # joined corresponding author