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Table of Contents

June 2023 | Volume 6, No. 6

Research Articles

  • The TUDOR domain of SMN is an H3K79<sup>me1</sup> histone mark reader
    Open Access
    The TUDOR domain of SMN is an H3K79me1 histone mark reader

    Olivier Binda, Aimé Boris Kimenyi Ishimwe, Maxime Galloy, Karine Jacquet, Armelle Corpet, Amélie Fradet-Turcotte, Jocelyn Côté, Patrick Lomonte

    Olivier Binda ... Patrick Lomonte

    Published 7 March 2023

    The survival of motor neuron (SMN) protein is depleted in spinal muscular atrophy (SMA) pathology and herein defined as the first reader of histone H3 mono-methylated on lysine 79 through its central TUDOR domain.

  • The ERK activator, BCI, inhibits ciliogenesis and causes defects in motor behavior, ciliary gating, and cytoskeletal rearrangement
    Open Access
    The ERK activator, BCI, inhibits ciliogenesis and causes defects in motor behavior, ciliary gating, and cytoskeletal rearrangement

    Larissa L Dougherty, Soumita Dutta, Prachee Avasthi

    Larissa L Dougherty ... Prachee Avasthi

    Published 13 March 2023

    ERK1/2 not only controls the cell cycle but also has new roles impacting various mechanisms affecting ciliogenesis. DUSP6 inhibition activates ERK to immediately inhibit ciliary assembly and upstream pathways.

  • Potency assessment of IFNγ-producing SARS-CoV-2-specific T cells from COVID-19 convalescent subjects
    Open Access
    Potency assessment of IFNγ-producing SARS-CoV-2-specific T cells from COVID-19 convalescent subjects

    Rubén Gil-Bescós, Ainhoa Ostiz, Saioa Zalba, Ibai Tamayo, Eva Bandrés, Elvira Rojas-de-Miguel, Margarita Redondo, Amaya Zabalza, Natalia Ramírez

    Rubén Gil-Bescós ... Natalia Ramírez

    Published 20 March 2023

    SARS-CoV-2-specific T-cells from convalescent donors present phenotypical and functional characteristics that make them a suitable candidate for a future development of an advanced cellular therapy.

  • MicroRNAs in tear fluids predict underlying molecular changes associated with Alzheimer’s disease
    Open Access
    MicroRNAs in tear fluids predict underlying molecular changes associated with Alzheimer’s disease

    Printha Wijesinghe, Jeanne Xi, Jing Cui, Matthew Campbell, Wellington Pham, Joanne A Matsubara

    Printha Wijesinghe ... Joanne A Matsubara

    Published 20 March 2023

    This study demonstrated the translational potential of deregulated tear fluid miRNAs associated with amyloid beta production and proinflammation in a transgenic AD mouse model.

  • Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins
    Open Access
    Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins

    Carina Groh, Per Haberkant, Frank Stein, Sebastian Filbeck, Stefan Pfeffer, Mikhail M Savitski, Felix Boos, Johannes M Herrmann

    Carina Groh ... Johannes M Herrmann

    Published 20 March 2023

    The combination of thermal proteome profiling and pulsed SILAC labelling shows that mitochondrial dysfunction imprints a characteristic pattern on the abundance and thermal stability of the proteome.

  • Structure-based design and characterization of Parkin-activating mutations
    Open Access
    Structure-based design and characterization of Parkin-activating mutations

    Michael U Stevens, Nathalie Croteau, Mohamed A Eldeeb, Odetta Antico, Zhi Wei Zeng, Rachel Toth, Thomas M Durcan, Wolfdieter Springer, Edward A Fon, Miratul MK Muqit, Jean-François Trempe

    Michael U Stevens ... Jean-François Trempe

    Published 20 March 2023

    Parkin, an E3 ubiquitin ligase involved in Parkinson’s disease, is inactive in the basal state and is activated by PINK1 to mediate mitophagy. Here, we characterized 31 mutations and discovered three that activate Parkin and rescue loss of PINK1 phosphorylation.

  • Cell death and barrier disruption by clinically used iodine concentrations
    Open Access
    Cell death and barrier disruption by clinically used iodine concentrations

    Anne Steins, Christina Carroll, Fui Jiun Choong, Amee J George, Jin-Shu He, Kate M Parsons, Shouya Feng, Si Ming Man, Cathelijne Kam, Lex M van Loon, Perlita Poh, Rita Ferreira, Graham J Mann, Russell L Gruen, Katherine M Hannan, Ross D Hannan, Klaus-Martin Schulte

    Anne Steins ... Klaus-Martin Schulte

    Published 21 March 2023

    Clinically used concentrations of povidone-iodine (PVP-I) are toxic to eukaryotic cells by attacking the lipid bilayer and tight junctions with fast kinetics and urge the reappraisal of PVP-I use.

  • Filopodia-like protrusions of adjacent somatic cells shape the developmental potential of oocytes
    Open Access
    Filopodia-like protrusions of adjacent somatic cells shape the developmental potential of oocytes

    Flora Crozet, Gaëlle Letort, Rose Bulteau, Christelle Da Silva, Adrien Eichmuller, Anna Francesca Tortorelli, Joséphine Blévinal, Morgane Belle, Julien Dumont, Tristan Piolot, Aurélien Dauphin, Fanny Coulpier, Alain Chédotal, Jean-Léon Maître, Marie-Hélène Verlhac, Hugh J Clarke, Marie-Emilie Terret

    Flora Crozet ... Marie-Emilie Terret

    Published 21 March 2023

    Filopodia-like protrusions sent by the somatic cells to the oocyte play a role in the structural integrity of the germline–somatic complex, and regulate gene expression in the oocyte and thus its developmental potential and chances to produce a viable embryo.

  • Characterisation of the OTU domain deubiquitinase complement of <em>Toxoplasma gondii</em>
    Open Access
    Characterisation of the OTU domain deubiquitinase complement of Toxoplasma gondii

    Mary-Louise Wilde, Ushma Ruparel, Theresa Klemm, V Vern Lee, Dale J Calleja, David Komander, Christopher J Tonkin

    Mary-Louise Wilde ... Christopher J Tonkin

    Published 23 March 2023

    The OTU deubiquitinase family is expanded in Toxoplasma parasites, and members show preferences for Lys6-, Lys11-, Lys48-, and Lys63-linked ubiquitin chains, and additional specificity for NEDD8. AlphaFold-guided structural analysis reveals cryptic ubiquitin-binding domains with functional importance.

  • Interaction hub critical for telomerase recruitment and primer-template handling for catalysis
    Open Access
    Interaction hub critical for telomerase recruitment and primer-template handling for catalysis

    Shilpa Padmanaban, Valerie M Tesmer, Jayakrishnan Nandakumar

    Shilpa Padmanaban ... Jayakrishnan Nandakumar

    Published 24 March 2023

    By deleting, mutating, and adding back parts of the telomerase enzyme that extends chromosome ends, we uncover features important for its proper functioning in the cell.

  • Local tissue mechanics control cardiac pacemaker cell embryonic patterning
    Open Access
    Local tissue mechanics control cardiac pacemaker cell embryonic patterning

    Trevor Henley, Julie Goudy, Marietta Easterling, Carrie Donley, Robert Wirka, Michael Bressan

    Trevor Henley ... Michael Bressan

    Published 27 March 2023

    Microenvironmental patterning during sinoatrial node morphogenesis is critical for sustaining cardiac pacemaker cell function.

  • Crystal structures of dimeric and heptameric mtHsp60 reveal the mechanism of chaperonin inactivation
    Open Access
    Crystal structures of dimeric and heptameric mtHsp60 reveal the mechanism of chaperonin inactivation

    Meng-Cheng Lai, Hao-Yu Cheng, Sin-Hong Lew, Yu-An Chen, Chien-Hung Yu, Han-You Lin, Shih-Ming Lin

    Meng-Cheng Lai ... Shih-Ming Lin

    Published 27 March 2023

    The crystal structure of the dimeric mtHsp60 from grouper fish has been determined, revealing a symmetrical subunit interaction with an exchanged α-helix connecting the two subunits. This structure provides new insights into the conformational changes of this important chaperonin

  • The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5
    Open Access
    The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5

    Alba Tornero-Écija, Antonia Zapata-del-Baño, Laura Antón-Esteban, Olivier Vincent, Ricardo Escalante

    Alba Tornero-Écija ... Ricardo Escalante

    Published 28 March 2023

    Binding of sorting nexin SNX5 to the VAB domain of VPS13A mediates its recruitment to membrane contact sites between SNX5-containing endosomal membranes, mitochondria, and ER.

  • Reduced replication but increased interferon resistance of SARS-CoV-2 Omicron BA.1
    Open Access
    Reduced replication but increased interferon resistance of SARS-CoV-2 Omicron BA.1

    Rayhane Nchioua, Annika Schundner, Susanne Klute, Lennart Koepke, Maximilian Hirschenberger, Sabrina Noettger, Giorgio Fois, Fabian Zech, Alexander Graf, Stefan Krebs, Peter Braubach, Helmut Blum, Steffen Stenger, Dorota Kmiec, Manfred Frick, Frank Kirchhoff, Konstantin MJ Sparrer

    Rayhane Nchioua ... Konstantin MJ Sparrer

    Published 28 March 2023

    The SARS-CoV-2 Omicron BA.1 variant of concern is highly resistant against exogenous interferons, suggesting that effective innate immune evasion contributed to its success.

  • FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins
    Open Access
    FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins

    Yusun Jeon, Seong H Chow, Isabella Stuart, Ashley Weir, Amy TY Yeung, Christine Hale, Sushmita Sridhar, Gordon Dougan, James E Vince, Thomas Naderer

    Yusun Jeon ... Thomas Naderer

    Published 28 March 2023

    FBXO11 regulates the expression of the complement receptor C5aR1 and the inflammatory cytokine IL-1β, affecting how macrophages respond to Staphylococcus aureus pore–forming toxins.

  • The role of <em>Limch1</em> alternative splicing in skeletal muscle function
    Open Access
    The role of Limch1 alternative splicing in skeletal muscle function

    Matthew S Penna, Rong-Chi Hu, George G Rodney, Thomas A Cooper

    Matthew S Penna ... Thomas A Cooper

    Published 28 March 2023

    This works identifies a novel, alternatively spliced isoform of LIMCH1, that is, developmentally regulated and specific to skeletal muscle. Knocking out the six skeletal muscle–specific exons of LIMCH1 leads to impaired skeletal muscle function in vivo and ex vivo.

  • The role of the mitochondrial outer membrane protein SLC25A46 in mitochondrial fission and fusion
    Open Access
    The role of the mitochondrial outer membrane protein SLC25A46 in mitochondrial fission and fusion

    Jana Schuettpelz, Alexandre Janer, Hana Antonicka, Eric A Shoubridge

    Jana Schuettpelz ... Eric A Shoubridge

    Published 28 March 2023

    The mitochondrial outer membrane protein SLC25A46 localizes to mitochondrial fusion and fission sites, and loss of function alters mitochondrial morphology and oligomerization states of MFN2 and OPA1.

  • UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells
    Open Access
    UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells

    Chengyan Chen, Yanmin Shen, Luqian Li, Yaoxin Ren, Zhao-Qi Wang, Tangliang Li

    Chengyan Chen ... Tangliang Li

    Published 30 March 2023

    We generated a new Upf3a-inducible knockout mouse model and showed that UPF3A does not repress expressions of NMD target genes in embryonic stem cells, somatic fibroblasts, and multiple tissues from adult mice.

  • Bats experience age-related hearing loss (presbycusis)
    Open Access
    Bats experience age-related hearing loss (presbycusis)

    Yifat Chaya Tarnovsky, Shahar Taiber, Yomiran Nissan, Arjan Boonman, Yaniv Assaf, Gerald S Wilkinson, Karen B Avraham, Yossi Yovel

    Yifat Chaya Tarnovsky ... Yossi Yovel

    Published 30 March 2023

    Bats exhibited age-related hearing loss. Bats are exposed to immense conspecific noise, but the frequency-dependent hearing loss was not correlated to the noise.

  • RopB represses the transcription of <em>speB</em> in the absence of SIP in group A <em>Streptococcus</em>
    Open Access
    RopB represses the transcription of speB in the absence of SIP in group A Streptococcus

    Chuan Chiang-Ni, Yan-Wen Chen, Kai-Lin Chen, Jian-Xian Jiang, Yong-An Shi, Chih-Yun Hsu, Yi-Ywan M Chen, Chih-Ho Lai, Cheng-Hsun Chiu

    Chuan Chiang-Ni ... Cheng-Hsun Chiu

    Published 31 March 2023

    SIP-free RopB, in contrast to SpeB-inducing peptide (SIP)-bound RopB, is a transcriptional repressor of speB and mediates speB repression in the covS mutant.

  • <em>arfA</em> antisense RNA regulates MscL excretory activity
    Open Access
    arfA antisense RNA regulates MscL excretory activity

    Rosa Morra, Fenryco Pratama, Thomas Butterfield, Geizecler Tomazetto, Kate Young, Ruth Lopez, Neil Dixon

    Rosa Morra ... Neil Dixon

    Published 3 April 2023

    Bacteria coordinate how they respond to translation and osmotic stress by using antisense RNA crosstalk between the genes involved in the respective stress response pathways.

  • Dynamic changes of enhancer and super enhancer landscape in degenerated nucleus pulposus cells
    Open Access
    Dynamic changes of enhancer and super enhancer landscape in degenerated nucleus pulposus cells

    Guowang Li, Yuxiang Kang, Xiangling Feng, Guohua Wang, Yue Yuan, Zhenhua Li, Lilong Du, Baoshan Xu

    Guowang Li ... Baoshan Xu

    Published 3 April 2023

    Super-enhancers mediate inflammatory cascade and extracellular matrix remodeling in degenerated nucleus pulposus cells.

  • The ubiquitin-like modifier FAT10 is degraded by the 20S proteasome in vitro but not in cellulo
    Open Access
    The ubiquitin-like modifier FAT10 is degraded by the 20S proteasome in vitro but not in cellulo

    Franziska Oliveri, Steffen Johannes Keller, Heike Goebel, Gerardo Omar Alvarez Salinas, Michael Basler

    Franziska Oliveri ... Michael Basler

    Published 3 April 2023

    The ubiquitin-like modifier FAT10 is degraded by the 20S proteasome in vitro, whereas FAT10 degradation depends on the 26S proteasome in cellulo, shown by impairing 26S function via Rpt2 knockdown.

  • Validating organoid-derived human intestinal monolayers for personalized therapy in cystic fibrosis
    Open Access
    Validating organoid-derived human intestinal monolayers for personalized therapy in cystic fibrosis

    Liron Birimberg-Schwartz, Wan Ip, Claire Bartlett, Julie Avolio, Annelotte M Vonk, Tarini Gunawardena, Kai Du, Mohsen Esmaeili, Jeffrey M Beekman, Johanna Rommens, Lisa Strug, Christine E Bear, Theo J Moraes, Tanja Gonska

    Liron Birimberg-Schwartz ... Tanja Gonska

    Published 5 April 2023

    Ussing chamber studies of intestinal organoid monolayers compare favorably to established preclinical tools to assess individual responses to CFTR modulator drugs in people with cystic fibrosis.

  • Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs
    Open Access
    Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs

    Qiuzhong Zhou, Yuxi Jiang, Chaoqun Cai, Wen Li, Melvin Khee-Shing Leow, Yi Yang, Jin Liu, Dan Xu, Lei Sun

    Qiuzhong Zhou ... Lei Sun

    Published 5 April 2023

    The authors demonstrate the transcriptional codes that govern the expression of conserved long noncoding RNAs through multi-dimensional conservation analysis.

  • Retinitis pigmentosa–associated mutations in mouse Prpf8 cause misexpression of circRNAs and degeneration of cerebellar granule cells
    Open Access
    Retinitis pigmentosa–associated mutations in mouse Prpf8 cause misexpression of circRNAs and degeneration of cerebellar granule cells

    Michaela Krausová, Michaela Kreplová, Poulami Banik, Zuzana Cvačková, Jan Kubovčiak, Martin Modrák, Dagmar Zudová, Jiří Lindovský, Agnieszka Kubik-Zahorodna, Marcela Pálková, Michal Kolář, Jan Procházka, Radislav Sedláček, David Staněk

    Michaela Krausová ... David Staněk

    Published 5 April 2023

    This study shows that Prpf8 mutations associated with human retinal degeneration in mice alter circRNA expression in cerebellar granule cells and induce their apoptosis.

  • An OMA1 redox site controls mitochondrial homeostasis, sarcoma growth, and immunogenicity
    Open Access
    An OMA1 redox site controls mitochondrial homeostasis, sarcoma growth, and immunogenicity

    Richard Miallot, Virginie Millet, Yann Groult, Angelika Modelska, Lydie Crescence, Sandrine Roulland, Sandrine Henri, Bernard Malissen, Nicolas Brouilly, Laurence Panicot-Dubois, Renaud Vincentelli, Gerlind Sulzenbacher, Pascal Finetti, Aurélie Dutour, Jean-Yves Blay, François Bertucci, Franck Galland, Philippe Naquet

    Richard Miallot ... Philippe Naquet

    Published 5 April 2023

    This work describes how a mutation affecting mitochondrial metabolism in a sarcoma model induces protective immunity against the tumor and how this result might be relevant for sarcoma patients.

  • Small vault RNA1-2 modulates expression of cell membrane proteins through nascent RNA silencing
    Open Access
    Small vault RNA1-2 modulates expression of cell membrane proteins through nascent RNA silencing

    Adele Alagia, Jana Tereňová, Ruth F Ketley, Arianna Di Fazio, Irina Chelysheva, Monika Gullerova

    Adele Alagia ... Monika Gullerova

    Published 10 April 2023

    Dicer-dependent small non-coding vault RNA1-2 employs nascent RNA silencing to modulate the expression of a group of genes associated with membrane function.

  • Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma
    Open Access
    Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma

    Elena Panizza, Brandon D Regalado, Fangyu Wang, Ichiro Nakano, Nathaniel M Vacanti, Richard A Cerione, Marc A Antonyak

    Elena Panizza ... Marc A Antonyak

    Published 10 April 2023

    Glioma patients often relapse because of resistance to radiation therapy. The transfer of the metabolic enzyme NAMPT via microvesicles and the accompanying elevated levels of NAD are found to be a mechanism by which glioma cells become resistant to radiation.

  • EZH2 controls epicardial cell migration during heart development
    Open Access
    EZH2 controls epicardial cell migration during heart development

    Haobin Jiang, Lina Bai, Shen Song, Qianqian Yin, Anteng Shi, Bin Zhou, Hong Lian, Houzao Chen, Cheng-ran Xu, Yanchun Wang, Yu Nie, Shengshou Hu

    Haobin Jiang ... Shengshou Hu

    Published 10 April 2023

    EZH2 influences epicardial cell migration into the myocardium via TIMP3-dependent fine tuning of basement membrane degradation, which leads to cardiac malformations and embryonic lethality.

  • New botulinum neurotoxin constructs for treatment of chronic pain
    Open Access
    New botulinum neurotoxin constructs for treatment of chronic pain

    Charlotte Leese, Claire Christmas, Judit Mészáros, Stephanie Ward, Maria Maiaru, Stephen P Hunt, Bazbek Davletov

    Charlotte Leese ... Bazbek Davletov

    Published 11 April 2023

    A new technique to make therapeutic botulinum neurotoxins via isopeptide bonding is described. The novel elongated botulinum neurotoxin can treat nerve injury pain without causing muscle paralysis.

  • Sleep–wake patterns are altered with age, Prdm13 signaling in the DMH, and diet restriction in mice
    Open Access
    Sleep–wake patterns are altered with age, Prdm13 signaling in the DMH, and diet restriction in mice

    Shogo Tsuji, Cynthia S Brace, Ruiqing Yao, Yoshitaka Tanie, Hirobumi Tada, Nicholas Rensing, Seiya Mizuno, Julio Almunia, Yingyi Kong, Kazuhiro Nakamura, Takahisa Furukawa, Noboru Ogiso, Shinya Toyokuni, Satoru Takahashi, Michael Wong, Shin-ichiro Imai, Akiko Satoh

    Shogo Tsuji ... Akiko Satoh

    Published 12 April 2023

    This study found that age-associated sleep changes are ameliorated by DR in the presence of Prdm13 signaling in the DMH, suggesting Prdm13+ DMH neurons will be of great interest to explore a potential intervention on age-associated sleep changes.

  • Cognitive decline in diabetic mice predisposed to Alzheimer’s disease is greater than in wild type
    Open Access
    Cognitive decline in diabetic mice predisposed to Alzheimer’s disease is greater than in wild type

    Marta Carús-Cadavieco, Inés Berenguer López, Alba Montoro Canelo, Miguel A Serrano-Lope, Sandra González-de la Fuente, Begoña Aguado, Alba Fernández-Rodrigo, Takaomi C Saido, Ana Frank García, César Venero, José A Esteban, Francesc Guix, Carlos G Dotti

    Marta Carús-Cadavieco ... Carlos G Dotti

    Published 14 April 2023

    This work proposes that T2DM is particularly harmful to brain function in individuals with a genetic predisposition to neurodegenerative pathology via, among others, γ-secretase inhibition.

  • Yolk-deprived <em>Caenorhabditis elegans</em> secure brood size at the expense of competitive fitness
    Open Access
    Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness

    Ellen Geens, Pieter Van de Walle, Francesca Caroti, Rob Jelier, Christian Steuwe, Liliane Schoofs, Liesbet Temmerman

    Ellen Geens ... Liesbet Temmerman

    Published 14 April 2023

    Many egg-laying species lower fecundity when yolk is in short supply, but not C. elegans. They still produce abundant offspring, yet of decreased quality.

Methods

  • Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method
    Open Access
    Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method

    Jianqi Yang, Alison N DeVore, Daniel A Fu, Mackenzie M Spicer, Mengcheng Guo, Samantha G Thompson, Katelin E Ahlers-Dannen, Federica Polato, Andre Nussenzweig, Rory A Fisher

    Jianqi Yang ... Rory A Fisher

    Published 10 April 2023

    A novel, precise, rapid, and generalizable method to determine transgene zygosity in mice by allele-specific restriction enzyme digestion of PCR products from transgenes or homologous endogenous genes.

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Volume 6, No. 6
June 2023
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