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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
}

Diana D Moreno Santillán, Tanya M Lama, Yocelyn T Gutierrez Guerrero, Alexis M Brown, Paul Donat, Huabin Zhao, Stephen J Rossiter, Laurel R Yohe, Joshua H Potter, Emma Teeling, Sonja Vernes, Kalina T J Davies, Eugene W Myers, Graham M Hughes, Zixia Huang, Federico Hoffmann, Angelique P Corthals, David A Ray#, Liliana M Dávalos#
Large-scale Genome sampling reveals unique immunity and metabolic adaptations in Bats.
Mol. Ecol., Art. No. 10.1111/mec.16027 (2021)
PubMed Source   

Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.
@article{Santillán8089,
author={Diana D Moreno Santillán, Tanya M Lama, Yocelyn T Gutierrez Guerrero, Alexis M Brown, Paul Donat, Huabin Zhao, Stephen J Rossiter, Laurel R Yohe, Joshua H Potter, Emma Teeling, Sonja Vernes, Kalina T J Davies, Eugene W Myers, Graham M Hughes, Zixia Huang, Federico Hoffmann, Angelique P Corthals, David A Ray, Liliana M Dávalos},
title={Large-scale Genome sampling reveals unique immunity and metabolic adaptations in Bats.},
journal ={Molecular ecology},
volume={},
pages={null--null},
year=2021
}

Mareike A Jordan, Gaia Pigino
The structural basis of intraflagellar transport at a glance.
J Cell Sci, 134(12) Art. No. jcs247163 (2021)
PubMed Source   

The intraflagellar transport (IFT) system is a remarkable molecular machine used by cells to assemble and maintain the cilium, a long organelle extending from eukaryotic cells that gives rise to motility, sensing and signaling. IFT plays a critical role in building the cilium by shuttling structural components and signaling receptors between the ciliary base and tip. To provide effective transport, IFT-A and IFT-B adaptor protein complexes assemble into highly repetitive polymers, called IFT trains, that are powered by the motors kinesin-2 and IFT-dynein to move bidirectionally along the microtubules. This dynamic system must be precisely regulated to shuttle different cargo proteins between the ciliary tip and base. In this Cell Science at a Glance article and the accompanying poster, we discuss the current structural and mechanistic understanding of IFT trains and how they function as macromolecular machines to assemble the structure of the cilium.
@article{Jordan8087,
author={Mareike A Jordan, Gaia Pigino},
title={The structural basis of intraflagellar transport at a glance.},
journal ={Journal of cell science},
volume={134},
issue ={12},
pages={null--null},
year=2021
}

Cristina Chiva, Teresa Mendes Maia, Christian Panse, Karel Stejskal, Thibaut Douché, Mariette Matondo, Damarys Loew, Dominic Helm, Mandy Rettel, Karl Mechtler, Francis Impens, Paolo Nanni#, Anna Shevchenko#, Eduard Sabidó#
Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users.
EMBO Rep, 22(6) Art. No. e52626 (2021)
Open Access PubMed Source   

Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.
@article{Chiva8057,
author={Cristina Chiva, Teresa Mendes Maia, Christian Panse, Karel Stejskal, Thibaut Douché, Mariette Matondo, Damarys Loew, Dominic Helm, Mandy Rettel, Karl Mechtler, Francis Impens, Paolo Nanni, Anna Shevchenko, Eduard Sabidó},
title={Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users.},
journal ={EMBO reports},
volume={22},
issue ={6},
pages={null--null},
year=2021
}

Anneline Pinson#, Wieland Huttner#
Neocortex expansion in development and evolution-from genes to progenitor cell biology.
Curr Opin Cell Biol, 73 9-18 (2021)
PubMed Source   

The evolutionary expansion of the neocortex, the seat of higher cognitive functions in humans, is primarily due to an increased and prolonged proliferation of neural progenitor cells during development. Basal progenitors, and in particular basal radial glial cells, are thought to have a key role in the increased generation of neurons that constitutes a foundation of neocortex expansion. Recent studies have identified primate-specific and human-specific genes and changes in gene expression that promote increased proliferative capacity of cortical progenitors. In many cases, the cell biological basis underlying this increase has been uncovered. Model systems such as mouse, ferret, nonhuman primates, and cerebral organoids have been used to establish the relevance of these genes for neocortex expansion.
@article{Pinson8076,
author={Anneline Pinson, Wieland Huttner},
title={Neocortex expansion in development and evolution-from genes to progenitor cell biology.},
journal ={Current opinion in cell biology},
volume={73},
pages={9--18},
year=2021
}

Lara Campana, Hannah Esser, Meritxell Huch, Stuart J Forbes
Liver regeneration and inflammation: from fundamental science to clinical applications.
Nat Rev Mol Cell Biol, Art. No. 10.1038/s41580-021-00373-7 (2021)
PubMed Source   

Liver regeneration is a complex process involving the crosstalk of multiple cell types, including hepatocytes, hepatic stellate cells, endothelial cells and inflammatory cells. The healthy liver is mitotically quiescent, but following toxic damage or resection the cells can rapidly enter the cell cycle to restore liver mass and function. During this process of regeneration, epithelial and non-parenchymal cells respond in a tightly coordinated fashion. Recent studies have described the interaction between inflammatory cells and a number of other cell types in the liver. In particular, macrophages can support biliary regeneration, contribute to fibrosis remodelling by repressing hepatic stellate cell activation and improve liver regeneration by scavenging dead or dying cells in situ. In this Review, we describe the mechanisms of tissue repair following damage, highlighting the close relationship between inflammation and liver regeneration, and discuss how recent findings can help design novel therapeutic approaches.
@article{Campana8070,
author={Lara Campana, Hannah Esser, Meritxell Huch, Stuart J Forbes},
title={Liver regeneration and inflammation: from fundamental science to clinical applications.},
journal ={Nature reviews. Molecular cell biology},
volume={},
pages={null--null},
year=2021
}

Cristina Subiran Adrados, Qinghao Yu, Lizbeth Airais Bolaños Castro, Luis Alberto Rodriguez Cabrera, Maximina H Yun
Salamander-Eci: An optical clearing protocol for the three-dimensional exploration of regeneration.
Dev Dyn, 250(6) 902-915 (2021)
Open Access PubMed Source   

Salamander limb regeneration is a complex biological process that entails the orchestration of multiple cellular and molecular mechanisms in a three-dimensional space. Hence, a comprehensive understanding of this process requires whole-structure level explorations. Recent advances in imaging and optical clearing methods have transformed the study of regenerative phenomena, allowing the three-dimensional visualization of structures and entire organisms.
@article{Adrados7844,
author={Cristina Subiran Adrados, Qinghao Yu, Lizbeth Airais Bolaños Castro, Luis Alberto Rodriguez Cabrera, Maximina H Yun},
title={Salamander-Eci: An optical clearing protocol for the three-dimensional exploration of regeneration.},
journal ={Developmental dynamics : an official publication of the American Association of Anatomists},
volume={250},
issue ={6},
pages={902--915},
year=2021
}

Lizbeth Airais Bolaños-Castro, Hannah E Walters, Rubén Octavio García Vázquez, Maximina H Yun
Immunity in salamander regeneration: Where are we standing and where are we headed?
Dev Dyn, 250(6) 753-767 (2021)
Open Access PubMed Source   

Salamanders exhibit the most extensive regenerative repertoire among vertebrates, being able to accomplish scar-free healing and faithful regeneration of significant parts of the eye, heart, brain, spinal cord, jaws and gills, as well as entire appendages throughout life. The cellular and molecular mechanisms underlying salamander regeneration are currently under extensive examination, with the hope of identifying the key drivers in each context, understanding interspecies differences in regenerative capacity, and harnessing this knowledge in therapeutic settings. The immune system has recently emerged as a potentially critical player in regenerative responses. Components of both innate and adaptive immunity have been found at critical stages of regeneration in a range of salamander tissues. Moreover, functional studies have identified a requirement for macrophages during heart and limb regeneration. However, our knowledge of salamander immunity remains scarce, and a thorough definition of the precise roles played by its members is lacking. Here, we examine the evidence supporting roles for immunity in various salamander regeneration models. We pinpoint observations that need revisiting through modern genetic approaches, uncover knowledge gaps, and highlight insights from various model organisms that could guide future explorations toward an understanding of the functions of immunity in regeneration.
@article{Bolaños-Castro7818,
author={Lizbeth Airais Bolaños-Castro, Hannah E Walters, Rubén Octavio García Vázquez, Maximina H Yun},
title={Immunity in salamander regeneration: Where are we standing and where are we headed?},
journal ={Developmental dynamics : an official publication of the American Association of Anatomists},
volume={250},
issue ={6},
pages={753--767},
year=2021
}

Chentao Yang✳︎, Yang Zhou✳︎, Stephanie Marcus✳︎, Giulio Formenti, Lucie A Bergeron, Zhenzhen Song, Xupeng Bi, Juraj Bergman, Marjolaine Marie C Rousselle, Chengran Zhou, Long Zhou, Yuan Deng, Miaoquan Fang, Duo Xie, Yuanzhen Zhu, Shangjin Tan, Jacquelyn Mountcastle, Bettina Haase, Jennifer Balacco, Jonathan Wood, William Chow, Arang Rhie, Martin Pippel, Margaret M Fabiszak, Sergey Koren, Olivier Fedrigo, Winrich A Freiwald, Kerstin Howe, Huanming Yang, Adam M Phillippy, Mikkel Heide Schierup, Erich D Jarvis, Guojie Zhang
Evolutionary and biomedical insights from a marmoset diploid genome assembly.
Nature, 594(7862) 227-233 (2021)
Open Access PubMed Source   

The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research2,3. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome-much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10-8 per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.
@article{Yang8069,
author={Chentao Yang, Yang Zhou, Stephanie Marcus, Giulio Formenti, Lucie A Bergeron, Zhenzhen Song, Xupeng Bi, Juraj Bergman, Marjolaine Marie C Rousselle, Chengran Zhou, Long Zhou, Yuan Deng, Miaoquan Fang, Duo Xie, Yuanzhen Zhu, Shangjin Tan, Jacquelyn Mountcastle, Bettina Haase, Jennifer Balacco, Jonathan Wood, William Chow, Arang Rhie, Martin Pippel, Margaret M Fabiszak, Sergey Koren, Olivier Fedrigo, Winrich A Freiwald, Kerstin Howe, Huanming Yang, Adam M Phillippy, Mikkel Heide Schierup, Erich D Jarvis, Guojie Zhang},
title={Evolutionary and biomedical insights from a marmoset diploid genome assembly.},
journal ={Nature},
volume={594},
issue ={7862},
pages={227--233},
year=2021
}

Carla A C Gonçalves, Michael Larsen, Sascha Jung, Johannes Stratmann, Akiko Nakamura, Marit Leuschner, Lena Hersemann, Rashmiparvathi Keshara, Signe Perlman, Lene Lundvall, Lea Langhoff Thuesen, Kristine Juul Hare, Ido Amit, Anne Jørgensen, Yung Hae Kim, Antonio Del Sol, Anne Grapin-Botton
A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion.
Nat Commun, 12(1) Art. No. 3144 (2021)
Open Access PubMed Source   

Human organogenesis remains relatively unexplored for ethical and practical reasons. Here, we report the establishment of a single-cell transcriptome atlas of the human fetal pancreas between 7 and 10 post-conceptional weeks of development. To interrogate cell-cell interactions, we describe InterCom, an R-Package we developed for identifying receptor-ligand pairs and their downstream effects. We further report the establishment of a human pancreas culture system starting from fetal tissue or human pluripotent stem cells, enabling the long-term maintenance of pancreas progenitors in a minimal, defined medium in three-dimensions. Benchmarking the cells produced in 2-dimensions and those expanded in 3-dimensions to fetal tissue identifies that progenitors expanded in 3-dimensions are transcriptionally closer to the fetal pancreas. We further demonstrate the potential of this system as a screening platform and identify the importance of the EGF and FGF pathways controlling human pancreas progenitor expansion.
@article{Gonçalves8060,
author={Carla A C Gonçalves, Michael Larsen, Sascha Jung, Johannes Stratmann, Akiko Nakamura, Marit Leuschner, Lena Hersemann, Rashmiparvathi Keshara, Signe Perlman, Lene Lundvall, Lea Langhoff Thuesen, Kristine Juul Hare, Ido Amit, Anne Jørgensen, Yung Hae Kim, Antonio Del Sol, Anne Grapin-Botton},
title={A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion.},
journal ={Nature communications},
volume={12},
issue ={1},
pages={null--null},
year=2021
}


✳︎ joined first author, # joined corresponding author