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Tatiana Tiago, Barbara Hummel, Federica F Morelli, Valentina Basile, Jonathan Vinet, Veronica Galli, Laura Mediani, Francesco Antoniani, Silvia Pomella, Matteo Cassandri, Maria Giovanna Garone, Beatrice Silvestri, Marco Cimino, Giovanna Cenacchi, Roberta Costa, Vincent Mouly, Ina Poser, Esti Yeger-Lotem, Alessandro Rosa, Simon Alberti, Rossella Rota, Anat Ben-Zvi, Ritwick Sawarkar, Serena Carra
Small heat-shock protein HSPB3 promotes myogenesis by regulating the lamin B receptor.
Cell Death Dis, 12(5) Art. No. 452 (2021)
Open Access PubMed Source   

One of the critical events that regulates muscle cell differentiation is the replacement of the lamin B receptor (LBR)-tether with the lamin A/C (LMNA)-tether to remodel transcription and induce differentiation-specific genes. Here, we report that localization and activity of the LBR-tether are crucially dependent on the muscle-specific chaperone HSPB3 and that depletion of HSPB3 prevents muscle cell differentiation. We further show that HSPB3 binds to LBR in the nucleoplasm and maintains it in a dynamic state, thus promoting the transcription of myogenic genes, including the genes to remodel the extracellular matrix. Remarkably, HSPB3 overexpression alone is sufficient to induce the differentiation of two human muscle cell lines, LHCNM2 cells, and rhabdomyosarcoma cells. We also show that mutant R116P-HSPB3 from a myopathy patient with chromatin alterations and muscle fiber disorganization, forms nuclear aggregates that immobilize LBR. We find that R116P-HSPB3 is unable to induce myoblast differentiation and instead activates the unfolded protein response. We propose that HSPB3 is a specialized chaperone engaged in muscle cell differentiation and that dysfunctional HSPB3 causes neuromuscular disease by deregulating LBR.
@article{Tiago8044,
author={Tatiana Tiago, Barbara Hummel, Federica F Morelli, Valentina Basile, Jonathan Vinet, Veronica Galli, Laura Mediani, Francesco Antoniani, Silvia Pomella, Matteo Cassandri, Maria Giovanna Garone, Beatrice Silvestri, Marco Cimino, Giovanna Cenacchi, Roberta Costa, Vincent Mouly, Ina Poser, Esti Yeger-Lotem, Alessandro Rosa, Simon Alberti, Rossella Rota, Anat Ben-Zvi, Ritwick Sawarkar, Serena Carra},
title={Small heat-shock protein HSPB3 promotes myogenesis by regulating the lamin B receptor.},
journal ={Cell death & disease},
volume={12},
issue ={5},
pages={null--null},
year=2021
}

Vita Stepanova✳︎, Kaja Ewa Moczulska✳︎, Guido Vacano✳︎, Ilia Kurochkin✳︎, Xiangchun Ju✳︎, Stephan Riesenberg, Dominik Macak, Tomislav Maricic, Linda Dombrowski, Maria Schörnig, Konstantinos Anastassiadis, Oliver Baker, Ronald Naumann, Ekaterina Khrameeva, Anna Vanushkina, Elena Stekolshchikova, Alina Egorova, Anna Tkachev, Randall Mazzarino, Nathan Duval, Dmitri Zubkov, Patrick Giavalisco, Terry G Wilkinson Ii, David Patterson, Philipp Khaitovich, Svante Pääbo
Reduced purine biosynthesis in humans after their divergence from Neandertals.
Elife, 10 Art. No. e58741 (2021)
Open Access PubMed Source   

We analyze the metabolomes of humans, chimpanzees and macaques in muscle, kidney and three different regions of the brain. Whereas several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans.
@article{Stepanova8039,
author={Vita Stepanova, Kaja Ewa Moczulska, Guido Vacano, Ilia Kurochkin, Xiangchun Ju, Stephan Riesenberg, Dominik Macak, Tomislav Maricic, Linda Dombrowski, Maria Schörnig, Konstantinos Anastassiadis, Oliver Baker, Ronald Naumann, Ekaterina Khrameeva, Anna Vanushkina, Elena Stekolshchikova, Alina Egorova, Anna Tkachev, Randall Mazzarino, Nathan Duval, Dmitri Zubkov, Patrick Giavalisco, Terry G Wilkinson Ii, David Patterson, Philipp Khaitovich, Svante Pääbo},
title={Reduced purine biosynthesis in humans after their divergence from Neandertals.},
journal ={eLife},
volume={10},
pages={null--null},
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, 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={},
pages={null--null},
year=2021
}

Giulio Formenti#, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane A McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S Horner, Eugene W Myers, Richard Durbin, Alessandro Achilli, Edward L Braun, Adam M Phillippy, Erich D Jarvis#, Erich D null
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
Genome Biol, 22(1) Art. No. 120 (2021)
Open Access PubMed Source   

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
@article{Formenti8035,
author={Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane A McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S Horner, Eugene W Myers, Richard Durbin, Alessandro Achilli, Edward L Braun, Adam M Phillippy, Erich D Jarvis, Erich D null},
title={Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.},
journal ={Genome biology},
volume={22},
issue ={1},
pages={null--null},
year=2021
}

Maximina H Yun#, Toshinori Hayashi#, Andras Simon#
Standardised gene and genetic nomenclature for the newt Pleurodeles waltl.
Dev Dyn, Art. No. doi: 10.1002/dvdy.355 (2021)
Open Access PubMed Source   

The Iberian ribbed newt, Pleurodeles waltl, has long been an important model for regenerative and developmental biology studies. The sequencing of its genome and the establishment of genetically-modified animals through transgenesis and gene-editing protocols have led to the generation of significant transgenic resources, whose numbers are rapidly expanding. Thus, there is an evident need for a harmonized nomenclature among salamander species. Nowoshilow et al propose a set of nomenclature guidelines for the laboratory axolotl. Here, we recommend its adoption by the P. waltl research community. This article is protected by copyright. All rights reserved.
@article{Yun8036,
author={Maximina H Yun, Toshinori Hayashi, Andras Simon},
title={Standardised gene and genetic nomenclature for the newt Pleurodeles waltl.},
journal ={Developmental dynamics : an official publication of the American Association of Anatomists},
volume={},
pages={null--1},
year=2021
}

Jodie Ouahed✳︎#, Judith R Kelsen✳︎#, Waldo A Spessott, Kameron Kooshesh, Maria L Sanmillan, Noor Dawany, Kathleen E Sullivan, Kathryn Hamilton, Voytek Slowik, Sergey Nejentsev, João Farela Neves, Helena Flores, Wendy K Chung, Ashley Wilson, Kwame Anyane Yeboa, Karen Wou, Preti Jain, Michael Field, Sophia Tollefson, Maiah H Dent, Dalin Li, Takeo Naito, Dermot P B McGovern, Andrew C Kwong, Faith Taliaferro, Jose Ordovas-Montanes, Bruce Horwitz, Daniel Kotlarz, Christoph Klein, Jonathan Evans, Jill Dorsey, Neil Warner, Abdul Elkadri, Aleixo M Muise, Jeffrey Goldsmith, Benjamin Thompson, Karin R Engelhardt, Andrew J Cant, Sophie Hambleton, Andrew Barclay, Agnes Toth-Petroczy, Dana Vuzman, Nikkola Carmichael, Corneliu Bodea, Christopher Cassa, Marcella Devoto, Richard L Maas, Edward M Behrens, Claudio G Giraudo#, Scott B Snapper#
Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation.
J Crohns Colitis, Art. No. doi: 10.1093/ecco-jcc/jjab077 (2021)
PubMed Source   

Very early onset inflammatory bowel disease (VEOIBD) is characterized by intestinal inflammation affecting infants and children less than 6 years of age. To date, over 60 monogenic etiologies of VEOIBD have been identified, many characterized by highly penetrant recessive or dominant variants in underlying immune and/or epithelial pathways. We sought to identify the genetic cause of VEOIBD in a subset of patients with a unique clinical presentation.
@article{Ouahed8031,
author={Jodie Ouahed, Judith R Kelsen, Waldo A Spessott, Kameron Kooshesh, Maria L Sanmillan, Noor Dawany, Kathleen E Sullivan, Kathryn Hamilton, Voytek Slowik, Sergey Nejentsev, João Farela Neves, Helena Flores, Wendy K Chung, Ashley Wilson, Kwame Anyane Yeboa, Karen Wou, Preti Jain, Michael Field, Sophia Tollefson, Maiah H Dent, Dalin Li, Takeo Naito, Dermot P B McGovern, Andrew C Kwong, Faith Taliaferro, Jose Ordovas-Montanes, Bruce Horwitz, Daniel Kotlarz, Christoph Klein, Jonathan Evans, Jill Dorsey, Neil Warner, Abdul Elkadri, Aleixo M Muise, Jeffrey Goldsmith, Benjamin Thompson, Karin R Engelhardt, Andrew J Cant, Sophie Hambleton, Andrew Barclay, Agnes Toth-Petroczy, Dana Vuzman, Nikkola Carmichael, Corneliu Bodea, Christopher Cassa, Marcella Devoto, Richard L Maas, Edward M Behrens, Claudio G Giraudo, Scott B Snapper},
title={Variants in STXBP3 Are Associated With Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation.},
journal ={Journal of Crohn's & colitis},
volume={},
pages={1--1},
year=2021
}

Lina Muhandes, Maria Chapsa, Martin Pippel, Rayk Behrendt, Yan Ge, Andreas Dahl, Buqing Yi, Alexander Dalpke, Sylke Winkler, Michael Hiller, Sebastien Boutin, Stefan Beissert, Rolf Jessberger, Padraic G Fallon, Axel Roers
Low threshold for cutaneous allergen sensitization but no spontaneous dermatitis or atopy in filaggrin-deficient mice.
J. Invest. Dermatol., Art. No. doi: 10.1016/j.jid.2021.02.763 (2021)
PubMed Source   

Loss of filaggrin (FLG) causes Ichthyosis vulgaris. Reduced filaggrin expression compromises epidermal barrier function and is associated with atopic dermatitis, allergy and asthma. The flaky tail mouse harbors two mutations that affect the skin barrier, Flgft, resulting in hypomorphic FLG expression, and Tmem79matted inactivating transmembrane protein 79. Mice defective only for Tmem79 featured dermatitis and systemic atopy, but also Flgft/ft BALB/c congenic mice developed eczema, high IgE and spontaneous asthma, suggesting that Flg protects from atopy. In contrast, a targeted Flg knock out mutation backcrossed to BALB/c did not result in dermatits or atopy. To resolve this discrepancy, we generated Flg-deficient mice on pure BALB/c background by inactivating Flg in BALB/c embryos. These animals feature an ichthyosis phenotype, barrier defect and facilitated percutaneous sensitization. However, they do not develop dermatitis or atopy. Whole genome sequencing of the atopic Flgft BALB/c congenics revealed that they were homozygous for the atopy-causing Tmem79matted mutation. In summary, we show that Flg-deficiency does not cause atopy in mice, in line with lack of atopic disease in a fraction of Ichthyosis vulgaris patients carrying two FLG null alleles. However, absence of FLG likely promotes and modulates dermatitis caused by other genetic barrier defects.
@article{Muhandes8028,
author={Lina Muhandes, Maria Chapsa, Martin Pippel, Rayk Behrendt, Yan Ge, Andreas Dahl, Buqing Yi, Alexander Dalpke, Sylke Winkler, Michael Hiller, Sebastien Boutin, Stefan Beissert, Rolf Jessberger, Padraic G Fallon, Axel Roers},
title={Low threshold for cutaneous allergen sensitization but no spontaneous dermatitis or atopy in filaggrin-deficient mice.},
journal ={The Journal of investigative dermatology},
volume={},
pages={1--1},
year=2021
}

Lucas von Chamier, Romain F Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loic Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
Democratising deep learning for microscopy with ZeroCostDL4Mic.
Nat Commun, 12(1) 2276-2276 (2021)
Open Access PubMed Source   

Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to train DL networks leads to an accessibility barrier that novice users often find difficult to overcome. Here, we present ZeroCostDL4Mic, an entry-level platform simplifying DL access by leveraging the free, cloud-based computational resources of Google Colab. ZeroCostDL4Mic allows researchers with no coding expertise to train and apply key DL networks to perform tasks including segmentation (using U-Net and StarDist), object detection (using YOLOv2), denoising (using CARE and Noise2Void), super-resolution microscopy (using Deep-STORM), and image-to-image translation (using Label-free prediction - fnet, pix2pix and CycleGAN). Importantly, we provide suitable quantitative tools for each network to evaluate model performance, allowing model optimisation. We demonstrate the application of the platform to study multiple biological processes.
@article{Chamier8030,
author={Lucas von Chamier, Romain F Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loic Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques},
title={Democratising deep learning for microscopy with ZeroCostDL4Mic.},
journal ={Nature communications},
volume={12},
issue ={1},
pages={2276--2276},
year=2021
}

Flaminia Kaluthantrige Don, Meritxell Huch
Organoids, Where We Stand and Where We Go.
Trends Mol Med, 27(5) 416-418 (2021)
PubMed Source   

Organoid cultures hold the promise of transforming basic and clinical research. Here, we provide a storyline of the highlights and breakthroughs that have an impact in present clinical research. We also discuss the bottlenecks that delay their full exploitation for the next generation of biomedical research.
@article{Don8029,
author={Flaminia Kaluthantrige Don, Meritxell Huch},
title={Organoids, Where We Stand and Where We Go.},
journal ={Trends in molecular medicine},
volume={27},
issue ={5},
pages={416--418},
year=2021
}

Suryanarayana Maddu, Bevan Cheeseman, Christian L. Müller, Ivo F. Sbalzarini
Learning physically consistent differential equation models from data using group sparsity.
Phys Rev E, 103(4) Art. No. 042310 (2021)
Open Access   Source   

We propose a statistical learning framework based on group-sparse regression that can be used to (i) enforce conservation laws, (ii) ensure model equivalence, and (iii) guarantee symmetries when learning or inferring differential-equation models from data. Directly learning interpretable mathematical models from data has emerged as a valuable modeling approach. However, in areas such as biology, high noise levels, sensor-induced correlations, and strong intersystem variability can render data-driven models nonsensical or physically inconsistent without additional constraints on the model structure. Hence, it is important to leverage prior knowledge from physical principles to learn biologically plausible and physically consistent models rather than models that simply fit the data best. We present the group iterative hard thresholding algorithm and use stability selection to infer physically consistent models with minimal parameter tuning. We show several applications from systems biology that demonstrate the benefits of enforcing priors in data-driven modeling.
@article{Maddu8008,
author={Suryanarayana Maddu, Bevan Cheeseman, Christian L. Müller, Ivo F. Sbalzarini},
title={Learning physically consistent differential equation models from data using group sparsity.},
journal ={Physical Review E},
volume={103},
issue ={4},
pages={1--1},
year=2021
}


✳︎ joined first author, # joined corresponding author