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Tiffany A Kosch✳︎#, María Torres-Sánchez✳︎#, H Christoph Liedtke, Kyle Summers, Maximina H Yun, Andrew J Crawford, Simon T Maddock, Md Sabbir Ahammed, Victor L N Araújo, Lorenzo V Bertola, Gary M Bucciarelli, Albert Carné, Céline M Carneiro, Kin O Chan, Ying Chen, Angelica Crottini, Jessica M da Silva, Robert D Denton, Carolin Dittrich, Gonçalo Espregueira Themudo, Katherine A Farquharson, Natalie J Forsdick, Edward Gilbert, Jing Che, Barbara A Katzenback, Ramachandran Kotharambath, Nicholas A Levis, Roberto Márquez, Glib Mazepa, Kevin P Mulder, Hendrik Müller, Mary J O'Connell, Pablo Orozco-terWengel, Gemma Palomar, Alice Petzold, David W Pfennig, Karin S Pfennig, Michael S Reichert, Jacques Robert, Mark D Scherz, Karen Siu-Ting, Anthony A Snead, Matthias Stöck, Adam M M Stuckert, Jennifer L Stynoski, Rebecca D Tarvin, Katharina C Wollenberg Valero
The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.
BMC Genomics, 25(1) Art. No. 1025 (2024)
Open Access PubMed Source   

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.
@article{Kosch8834,
author={Tiffany A Kosch, María Torres-Sánchez, H Christoph Liedtke, Kyle Summers, Maximina H Yun, Andrew J Crawford, Simon T Maddock, Md Sabbir Ahammed, Victor L N Araújo, Lorenzo V Bertola, Gary M Bucciarelli, Albert Carné, Céline M Carneiro, Kin O Chan, Ying Chen, Angelica Crottini, Jessica M da Silva, Robert D Denton, Carolin Dittrich, Gonçalo Espregueira Themudo, Katherine A Farquharson, Natalie J Forsdick, Edward Gilbert, Jing Che, Barbara A Katzenback, Ramachandran Kotharambath, Nicholas A Levis, Roberto Márquez, Glib Mazepa, Kevin P Mulder, Hendrik Müller, Mary J O'Connell, Pablo Orozco-terWengel, Gemma Palomar, Alice Petzold, David W Pfennig, Karin S Pfennig, Michael S Reichert, Jacques Robert, Mark D Scherz, Karen Siu-Ting, Anthony A Snead, Matthias Stöck, Adam M M Stuckert, Jennifer L Stynoski, Rebecca D Tarvin, Katharina C Wollenberg Valero},
title={The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.},
journal ={BMC genomics},
volume={25},
issue ={1},
pages={null--null},
year=2024
}

Kathryn Turnbull#, Helge Paternoga, Esther von der Weth, Artyom A Egorov, Agnieszka A Pochopien, Yujie Zhang, Lilit Nersisyan, Tõnu Margus, Marcus J O Johansson, Vicent Pelechano, Daniel N Wilson#, Vasili Hauryliuk#
The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.
Nucleic Acids Res, 52(19) 12005-12020 (2024)
Open Access PubMed Source Full Text   

The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.
@article{Turnbull8793,
author={Kathryn Turnbull, Helge Paternoga, Esther von der Weth, Artyom A Egorov, Agnieszka A Pochopien, Yujie Zhang, Lilit Nersisyan, Tõnu Margus, Marcus J O Johansson, Vicent Pelechano, Daniel N Wilson, Vasili Hauryliuk},
title={The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.},
journal ={Nucleic acids research},
volume={52},
issue ={19},
pages={12005--12020},
year=2024
}

Máire Ní Leathlobhair#, Anna Frangou, Ben Kinnersley, Alex J Cornish, Daniel Chubb, Eszter Lakatos, Prabhu Arumugam, Andreas J Gruber, Philip Law, Avraam Tapinos, G Maria Jakobsdottir, Iliana Peneva, Atef Sahli, Evie M Smyth, Richard Y Ball, Rushan Sylva, Ksenija Benes, Dan Stark, Robin J Young, Alexander T J Lee, Vincent Wolverson, Richard S Houlston, Alona Sosinsky, Andrew Protheroe, Matthew J Murray#, David C Wedge#, Clare Verrill#, Testicular Cancer Genomics England Clinical Interpretation Partnership Consortium; Genomics England Research Consortium
Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project.
Nat Commun, 15(1) Art. No. 9247 (2024)
Open Access PubMed Source   

Testicular germ cell tumours (TGCT), which comprise seminoma and non-seminoma subtypes, are the most common cancers in young men. In this study, we present a comprehensive whole genome sequencing analysis of adult TGCTs. Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. This catalogue offers a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genome features, including mutational signatures and analysis of extrachromosomal DNA amplification. This study establishes correlations between genomic alterations and histological diversification, revealing divergent evolutionary trajectories among TGCT subtypes. By reconstructing the chronological order of driver events, we identify a subgroup of adult TGCTs undergoing relatively late whole genome duplication. Additionally, we present evidence that human leukocyte antigen loss is a more prevalent mechanism of immune disruption in seminomas. Collectively, our findings provide valuable insights into the developmental and immune modulatory processes implicated in TGCT pathogenesis and progression.
@article{Leathlobhair8828,
author={Máire Ní Leathlobhair, Anna Frangou, Ben Kinnersley, Alex J Cornish, Daniel Chubb, Eszter Lakatos, Prabhu Arumugam, Andreas J Gruber, Philip Law, Avraam Tapinos, G Maria Jakobsdottir, Iliana Peneva, Atef Sahli, Evie M Smyth, Richard Y Ball, Rushan Sylva, Ksenija Benes, Dan Stark, Robin J Young, Alexander T J Lee, Vincent Wolverson, Richard S Houlston, Alona Sosinsky, Andrew Protheroe, Matthew J Murray, David C Wedge, Clare Verrill, Testicular Cancer Genomics England Clinical Interpretation Partnership Consortium; Genomics England Research Consortium},
title={Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project.},
journal ={Nature communications},
volume={15},
issue ={1},
pages={null--null},
year=2024
}

Matthias Lutolf, Milica Radisic, Jeffrey Beekman, Dan Dongeun Huh, Meritxell Huch, Margherita Yayoi Turco, Zeinab Niloofar Tahmasebi Birgani, Dong Gao, Rui Yao, Hang Lin, Takanori Takebe
In vitro human cell-based models : What can they do and what are their limitations?
Trends Biotechnol, Art. No. doi: 10.1016/j.tibtech.2024.08.015 (2024)
PubMed Source  

@article{Lutolf8837,
author={Matthias Lutolf, Milica Radisic, Jeffrey Beekman, Dan Dongeun Huh, Meritxell Huch, Margherita Yayoi Turco, Zeinab Niloofar Tahmasebi Birgani, Dong Gao, Rui Yao, Hang Lin, Takanori Takebe},
title={In vitro human cell-based models : What can they do and what are their limitations?},
journal ={Trends in biotechnology},
volume={},
pages={1--1},
year=2024
}

Benjamin R Sabari#, Anthony Hyman#, Denes Hnisz
Functional specificity in biomolecular condensates revealed by genetic complementation.
Nat Rev Genet, Art. No. doi: 10.1038/s41576-024-00780-4 (2024)
PubMed Source   

Biomolecular condensates are thought to create subcellular microenvironments that regulate specific biochemical activities. Extensive in vitro work has helped link condensate formation to a wide range of cellular processes, including gene expression, nuclear transport, signalling and stress responses. However, testing the relationship between condensate formation and function in cells is more challenging. In particular, the extent to which the cellular functions of condensates depend on the nature of the molecular interactions through which the condensates form is a major outstanding question. Here, we review results from recent genetic complementation experiments in cells, and highlight how genetic complementation provides important insights into cellular functions and functional specificity of biomolecular condensates. Combined with observations from human genetic disease, these experiments suggest that diverse condensate-promoting regions within cellular proteins confer different condensate compositions, biophysical properties and functions.
@article{Sabari8827,
author={Benjamin R Sabari, Anthony Hyman, Denes Hnisz},
title={Functional specificity in biomolecular condensates revealed by genetic complementation.},
journal ={Nature reviews. Genetics},
volume={},
pages={1--1},
year=2024
}

Bassam Aljani, Annette I Garbe, Eva-Maria Sedlmeier, Ramona Lickert, Fabian Rost, Anette-Gabriele Ziegler, Enzio Bonifacio, Anne Eugster
Gene expression profiles in placenta and their association with anesthesia, delivery mode and maternal diabetes.
Placenta, 158 126-135 (2024)
Open Access PubMed Source   

Fetal development is dependent on placenta and affected by multiple factors including maternal diabetes. Here we aimed to identify maternal diabetes-associated changes in placentas and analyzed placental gene expression to understand its modulation by maternal diabetes and birth mode.
@article{Aljani8830,
author={Bassam Aljani, Annette I Garbe, Eva-Maria Sedlmeier, Ramona Lickert, Fabian Rost, Anette-Gabriele Ziegler, Enzio Bonifacio, Anne Eugster},
title={Gene expression profiles in placenta and their association with anesthesia, delivery mode and maternal diabetes.},
journal ={Placenta},
volume={158},
pages={126--135},
year=2024
}

Chi Fung Willis Chow, Soumyadeep Ghosh, Anna Hadarovich, Agnes Toth-Petroczy
SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.
Proc Natl Acad Sci U.S.A., 121(42) Art. No. e2401622121 (2024)
Open Access PubMed Source   

Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite them comprising ~21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment-based approaches in assessing evolutionary homology in unalignable sequences. Furthermore, it correctly identified dissimilar but functionally analogous IDRs in IDR-replacement experiments reported in the literature, whereas alignment-based tools were incapable of detecting such functional relationships. SHARK-dive not only predicts functionally similar IDRs at a proteome-wide scale but also identifies cryptic sequence properties and motifs that drive remote homology and analogy, thereby providing interpretable and experimentally verifiable hypotheses of the sequence determinants that underlie such relationships. SHARK-dive acts as an alternative to alignment to facilitate systematic analysis and functional annotation of the unalignable protein universe.
@article{Chow8819,
author={Chi Fung Willis Chow, Soumyadeep Ghosh, Anna Hadarovich, Agnes Toth-Petroczy},
title={SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={121},
issue ={42},
pages={null--null},
year=2024
}

Lennart J. Schulze, Sachin K. T. Veettil, Ivo F. Sbalzarini
A high-order fully Lagrangian particle level-set method for dynamic surfaces.
J Comput Phys, 515 Art. No. 113262 (2024)
Open Access   Source   

We present a fully Lagrangian particle level-set method based on high-order polynomial regression. This enables meshfree simulations of dynamic surfaces, relaxing the need for particle-mesh interpolation. Instead, we perform level-set redistancing directly on irregularly distributed particles by polynomial regression in a Newton-Lagrange basis on a set of unisolvent nodes. We demonstrate that the resulting particle closest-point (PCP) redistancing achieves high-order accuracy for 2D and 3D geometries discretized on irregular particle distributions and has better robustness against particle distortion than regression in a monomial basis. Further, we show convergence in classic level-set benchmark cases involving ill-conditioned particle distributions, and we present an example application to multi-phase flow problems involving oscillating and dividing droplets.
@article{Schulze8766,
author={Lennart J. Schulze, Sachin K. T. Veettil, Ivo F. Sbalzarini},
title={A high-order fully Lagrangian particle level-set method for dynamic surfaces.},
journal ={Journal of Computational Physics},
volume={515},
pages={null--null},
year=2024
}

Dominica Cao, Sumit Garai, James DiFrisco#, Jesse V Veenvliet#
The logic of monsters: development and morphological diversity in stem-cell-based embryo models.
Interface Focus, 14(5) Art. No. 20240023 (2024)
Open Access PubMed Source   

Organoids and stem-cell-based embryo models (SEMs) are imperfect organ or embryo representations that explore a much larger space of possible forms, or morphospace, compared to their in vivo counterparts. Here, we discuss SEM biology in light of seminal work by Pere Alberch, a leading figure in early evo-devo, interpreting SEMs as developmental 'monstrosities' in the Alberchian sense. Alberch suggested that ordered patterns in aberrant development-i.e. 'the logic of monsters'-reveal developmental constraints on possible morphologies. In the same vein, we detail how SEMs have begun to shed light on structural features of normal development, such as developmental variability, the relative importance of internal versus external constraints, boundary conditions and design principles governing robustness and canalization. We argue that SEMs represent a powerful experimental tool to explore and expand developmental morphospace and propose that the 'monstrosity' of SEMs can be leveraged to uncover the 'hidden' rules and developmental constraints that robustly shape and pattern the embryo.
@article{Cao8831,
author={Dominica Cao, Sumit Garai, James DiFrisco, Jesse V Veenvliet},
title={The logic of monsters: development and morphological diversity in stem-cell-based embryo models.},
journal ={Interface focus},
volume={14},
issue ={5},
pages={null--null},
year=2024
}

Shanshan Xu, Maria E Gierisch, Enrica Barchi, Ina Poser, Simon Alberti, Florian A Salomons, Nico P Dantuma
Chemical inhibition of the integrated stress response impairs the ubiquitin-proteasome system.
Commun Biol, 7(1) Art. No. 1282 (2024)
Open Access PubMed Source   

Inhibitors of the integrated stress response (ISR) have been used to explore the potential beneficial effects of reducing the activation of this pathway in diseases. As the ISR is in essence a protective response, there is, however, a risk that inhibition may compromise the cell's ability to restore protein homeostasis. Here, we show that the experimental compound ISRIB impairs degradation of proteins by the ubiquitin-proteasome system (UPS) during proteotoxic stress in the cytosolic, but not nuclear, compartment. Accumulation of a UPS reporter substrate that is intercepted by ribosome quality control was comparable to the level observed after blocking the UPS with a proteasome inhibitor. Consistent with impairment of the cytosolic UPS, ISRIB treatment caused an accumulation of polyubiquitylated and detergent insoluble defective ribosome products (DRiPs) in the presence of puromycin. Our data suggest that the persistent protein translation during proteotoxic stress in the absence of a functional ISR increases the pool of DRiPs, thereby hindering the efficient clearance of cytosolic substrates by the UPS.
@article{Xu8822,
author={Shanshan Xu, Maria E Gierisch, Enrica Barchi, Ina Poser, Simon Alberti, Florian A Salomons, Nico P Dantuma},
title={Chemical inhibition of the integrated stress response impairs the ubiquitin-proteasome system.},
journal ={Communications biology},
volume={7},
issue ={1},
pages={null--null},
year=2024
}
✳︎ joint first authors, # joint corresponding authors
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