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Takeshi Takeuchi✳︎, Yoshihiko Suzuki✳︎, Shugo Watabe, Kosuke Nagai, Tetsuji Masaoka, Manabu Fujie, Mayumi Kawamitsu, Noriyuki Satoh, Eugene W Myers
A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.
DNA Res, 29(6) Art. No. doi: 10.1093/dnares/dsac035 (2022)
PubMed Source Full Text   

Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.
@article{Takeuchi8475,
author={Takeshi Takeuchi, Yoshihiko Suzuki, Shugo Watabe, Kosuke Nagai, Tetsuji Masaoka, Manabu Fujie, Mayumi Kawamitsu, Noriyuki Satoh, Eugene W Myers},
title={A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.},
journal ={DNA research : an international journal for rapid publication of reports on genes and genomes},
volume={29},
issue ={6},
pages={1--1},
year=2022
}

Keisuke Ishihara✳︎, Arghyadip Mukherjee✳︎, Elena Gromberg, Jan Brugués#, Elly M. Tanaka#, Frank Jülicher#
Topological morphogenesis of neuroepithelial organoids.
Nat Phys, Art. No. doi: 10.1038/s41567-022-01822-6 (2022)
Open Access Source Full Text   

Animal organs exhibit complex topologies involving cavities and tubular networks, which underlie their form and function. However, how topology emerges during the development of organ shape, or morphogenesis, remains elusive. Here we combine tissue reconstitution and quantitative microscopy to show that tissue topology and shape is governed by two distinct modes of topological transitions. One mode involves the fusion of two separate epithelia and the other involves the fusion of two ends of the same epithelium. The morphological space is captured by a single control parameter that can be traced back to the relative rates of the two epithelial fusion modes. Finally, we identify a pharmacologically accessible pathway that regulates the frequency of two modes of epithelial fusion, and demonstrate the control of organoid topology and shape. The physical principles uncovered here provide fundamental insights into the self-organization of complex tissues.
@article{Ishihara8227,
author={Keisuke Ishihara, Arghyadip Mukherjee, Elena Gromberg, Jan Brugués, Elly M. Tanaka, Frank Jülicher},
title={Topological morphogenesis of neuroepithelial organoids.},
journal ={Nature physics},
volume={},
pages={null--null},
year=2022
}

Tina Subic, Ivo F. Sbalzarini
A Gaussian jump process formulation of the reaction-diffusion master equation enables faster exact stochastic simulations.
J Chem Phys, 157(19) Art. No. 194110 (2022)
Open Access   PubMed Source   

We propose a Gaussian jump process model on a regular Cartesian lattice for the diffusion part of the Reaction-Diffusion Master Equation (RDME). We derive the resulting Gaussian RDME (GRDME) formulation from analogy with a kernel-based discretization scheme for continuous diffusion processes and quantify the limits of its validity relative to the classic RDME. We then present an exact stochastic simulation algorithm for the GRDME, showing that the accuracies of GRDME and RDME are comparable, but exact simulations of the GRDME require only a fraction of the computational cost of exact RDME simulations. We analyze the origin of this speedup and its scaling with problem dimension. The benchmarks suggest that the GRDME is a particularly beneficial model for diffusion-dominated systems in three dimensional spaces, often occurring in systems biology and cell biology.
@article{Subic8476,
author={Tina Subic, Ivo F. Sbalzarini},
title={A Gaussian jump process formulation of the reaction-diffusion master equation enables faster exact stochastic simulations.},
journal ={The Journal of chemical physics},
volume={157},
issue ={19},
pages={null--null},
year=2022
}

Caitlyn L McCafferty#, Ophelia Papoulas, Mareike A Jordan, Gabriel Hoogerbrugge, Candice Nichols, Gaia Pigino, David W Taylor, John Wallingford, Edward M Marcotte#
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex.
Elife, 11 Art. No. doi: 10.7554/eLife.81977 (2022)
Open Access PubMed Source   

Intraflagellar transport (IFT) is a conserved process of cargo transport in cilia that is essential for development and homeostasis in organisms ranging from algae to vertebrates. In humans, variants in genes encoding subunits of the cargo-adapting IFT-A and IFT-B protein complexes are a common cause of genetic diseases known as ciliopathies. While recent progress has been made in determining the atomic structure of IFT-B, little is known of the structural biology of IFT-A. Here, we combined chemical cross-linking mass spectrometry and cryo-electron tomography with AlphaFold2-based prediction of both protein structures and interaction interfaces to model the overall architecture of the monomeric six-subunit IFT-A complex, as well as its polymeric assembly within cilia. We define monomer-monomer contacts and membrane-associated regions available for association with transported cargo, and we also use this model to provide insights into the pleiotropic nature of human ciliopathy-associated genetic variants in genes encoding IFT-A subunits. Our work demonstrates the power of integration of experimental and computational strategies both for multi-protein structure determination and for understanding the etiology of human genetic disease.
@article{McCafferty8474,
author={Caitlyn L McCafferty, Ophelia Papoulas, Mareike A Jordan, Gabriel Hoogerbrugge, Candice Nichols, Gaia Pigino, David W Taylor, John Wallingford, Edward M Marcotte},
title={Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex.},
journal ={eLife},
volume={11},
pages={1--1},
year=2022
}

Jan Fischer✳︎, Eduardo Fernández Ortuño✳︎, Fabio Marsoner✳︎, Annasara Artioli, Jula Peters, Takashi Namba, Christina Eugster Oegema, Wieland Huttner#, Julia Ladewig#, Michael Heide#
Human-specific ARHGAP11B ensures human-like basal progenitor levels in hominid cerebral organoids.
EMBO Rep, 23(11) Art. No. e54728 (2022)
Open Access PubMed Source   

The human-specific gene ARHGAP11B has been implicated in human neocortex expansion. However, the extent of ARHGAP11B's contribution to this expansion during hominid evolution is unknown. Here we address this issue by genetic manipulation of ARHGAP11B levels and function in chimpanzee and human cerebral organoids. ARHGAP11B expression in chimpanzee cerebral organoids doubles basal progenitor levels, the class of cortical progenitors with a key role in neocortex expansion. Conversely, interference with ARHGAP11B's function in human cerebral organoids decreases basal progenitors down to the chimpanzee level. Moreover, ARHGAP11A or ARHGAP11B rescue experiments in ARHGAP11A plus ARHGAP11B double-knockout human forebrain organoids indicate that lack of ARHGAP11B, but not of ARHGAP11A, decreases the abundance of basal radial glia-the basal progenitor type thought to be of particular relevance for neocortex expansion. Taken together, our findings demonstrate that ARHGAP11B is necessary and sufficient to ensure the elevated basal progenitor levels that characterize the fetal human neocortex, suggesting that this human-specific gene was a major contributor to neocortex expansion during human evolution.
@article{Fischer8449,
author={Jan Fischer, Eduardo Fernández Ortuño, Fabio Marsoner, Annasara Artioli, Jula Peters, Takashi Namba, Christina Eugster Oegema, Wieland Huttner, Julia Ladewig, Michael Heide},
title={Human-specific ARHGAP11B ensures human-like basal progenitor levels in hominid cerebral organoids.},
journal ={EMBO reports},
volume={23},
issue ={11},
pages={1--1},
year=2022
}

Berna Sozen#, Deniz Conkar, Jesse V Veenvliet#
Carnegie in 4D? Stem-cell-based models of human embryo development.
Semin Cell Dev Biol, 131 44-57 (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={131},
pages={44--57},
year=2022
}

Sean P A Ritter, Logan A Brand, Shelby L Vincent, Albert Remus R Rosana, Allison Lewis, Denise S Whitford, George W Owttrim
Multiple Light-Dark Signals Regulate Expression of the DEAD-Box RNA Helicase CrhR in Synechocystis PCC 6803.
Cells, 11(21) Art. No. 3397 (2022)
Open Access PubMed Source   

Since oxygenic photosynthesis evolved in the common ancestor of cyanobacteria during the Archean, a range of sensing and response strategies evolved to allow efficient acclimation to the fluctuating light conditions experienced in the diverse environments they inhabit. However, how these regulatory mechanisms are assimilated at the molecular level to coordinate individual gene expression is still being elucidated. Here, we demonstrate that integration of a series of three distinct light signals generate an unexpectedly complex network regulating expression of the sole DEAD-box RNA helicase, CrhR, encoded in Synechocystis sp. PCC 6803. The mechanisms function at the transcriptional, translational and post-translation levels, fine-tuning CrhR abundance to permit rapid acclimation to fluctuating light and temperature regimes. CrhR abundance is enhanced 15-fold by low temperature stress. We initially confirmed that the primary mechanism controlling crhR transcript accumulation at 20 °C requires a light quantity-driven reduction of the redox poise in the vicinity of the plastoquinone pool. Once transcribed, a specific light quality cue, a red light signal, was required for crhR translation, far-red reversal of which indicates a phytochrome-mediated mechanism. Examination of CrhR repression at 30 °C revealed that a redox- and light quality-independent light signal was required to initiate CrhR degradation. The crucial role of light was further revealed by the observation that dark conditions superseded the light signals required to initiate each of these regulatory processes. The findings reveal an unexpected complexity of light-dark sensing and signaling that regulate expression of an individual gene in cyanobacteria, an integrated mechanism of environmental perception not previously reported.
@article{Ritter8479,
author={Sean P A Ritter, Logan A Brand, Shelby L Vincent, Albert Remus R Rosana, Allison Lewis, Denise S Whitford, George W Owttrim},
title={Multiple Light-Dark Signals Regulate Expression of the DEAD-Box RNA Helicase CrhR in Synechocystis PCC 6803.},
journal ={Cells},
volume={11},
issue ={21},
pages={null--null},
year=2022
}

Jonathan Bauermann✳︎, Sudarshana Laha✳︎, Patrick M McCall, Frank Jülicher#, Christoph A. Weber#
Chemical Kinetics and Mass Action in Coexisting Phases.
J Am Chem Soc, 144(42) 19294-19304 (2022)
PubMed Source   

The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At nondilute conditions, interactions among the components can give rise to coexisting phases, which can significantly alter the kinetics of chemical reactions. Here, we derive a theory for chemical reactions in coexisting phases at phase equilibrium. We show that phase equilibrium couples the rates of chemical reactions of components with their diffusive exchanges between the phases. Strikingly, the chemical relaxation kinetics can be represented as a flow along the phase equilibrium line in the phase diagram. A key finding of our theory is that differences in reaction rates between coexisting phases stem solely from phase-dependent reaction rate coefficients. Our theory is key to interpreting how concentration levels of reactive components in condensed phases control chemical reaction rates in synthetic and biological systems.
@article{Bauermann8477,
author={Jonathan Bauermann, Sudarshana Laha, Patrick M McCall, Frank Jülicher, Christoph A. Weber},
title={Chemical Kinetics and Mass Action in Coexisting Phases.},
journal ={Journal of the American Chemical Society},
volume={144},
issue ={42},
pages={19294--19304},
year=2022
}

Qinghao Yu✳︎, Hannah E Walters✳︎#, Maximina H Yun#
Induction and Characterization of Cellular Senescence in Salamanders.
Methods Mol Biol, 2562 Art. No. doi: 10.1007/978-1-0716-2659-7_8. (2022)
PubMed Source   

Cellular senescence is a permanent proliferation arrest mechanism induced following the detection of genotoxic stress. Mounting evidence has causally linked the accumulation of senescent cells to a growing number of age-related pathologies in mammals. However, recent data have also highlighted senescent cells as important mediators of tissue remodeling during organismal development, tissue repair, and regeneration. As powerful model organisms for studying such processes, salamanders constitute a system in which to probe the characteristics, physiological functions, and evolutionary facets of cellular senescence. In this chapter, we outline methods for the generation, identification, and characterization of salamander senescent cells in vitro and in vivo.
@article{Yu8463,
author={Qinghao Yu, Hannah E Walters, Maximina H Yun},
title={Induction and Characterization of Cellular Senescence in Salamanders.},
journal ={Methods in molecular biology (Clifton, N.J.)},
volume={2562},
pages={135--154},
year=2022
}

Keiichi Katsumoto#, Siham Yennek, Chunguang Chen, Luis Fernando Delgadillo Silva, Sofia Traikov, Dror Sever, Ajuna Azad, Jingdong Shan, Seppo Vainio, Nikolay Ninov, Stephan Speier, Anne Grapin-Botton#
Wnt4 is heterogeneously activated in maturing β-cells to control calcium signaling, metabolism and function.
Nat Commun, 13(1) Art. No. 6255 (2022)
Open Access PubMed Source   

Diabetes is a multifactorial disorder characterized by loss or dysfunction of pancreatic β-cells. β-cells are heterogeneous, exhibiting different glucose sensing, insulin secretion and gene expression. They communicate with other endocrine cell types via paracrine signals and between β-cells via gap junctions. Here, we identify the importance of signaling between β-cells via the extracellular signal WNT4. We show heterogeneity in Wnt4 expression, most strikingly in the postnatal maturation period, Wnt4-positive cells, being more mature while Wnt4-negative cells are more proliferative. Knock-out in adult β-cells shows that WNT4 controls the activation of calcium signaling in response to a glucose challenge, as well as metabolic pathways converging to lower ATP/ADP ratios, thereby reducing insulin secretion. These results reveal that paracrine signaling between β-cells is important in addition to gap junctions in controling insulin secretion. Together with previous reports of WNT4 up-regulation in obesity our observations suggest an adaptive insulin response coordinating β-cells.
@article{Katsumoto8465,
author={Keiichi Katsumoto, Siham Yennek, Chunguang Chen, Luis Fernando Delgadillo Silva, Sofia Traikov, Dror Sever, Ajuna Azad, Jingdong Shan, Seppo Vainio, Nikolay Ninov, Stephan Speier, Anne Grapin-Botton},
title={Wnt4 is heterogeneously activated in maturing β-cells to control calcium signaling, metabolism and function.},
journal ={Nature communications},
volume={13},
issue ={1},
pages={null--null},
year=2022
}
✳︎ joint first authors, # joint corresponding authors
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