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PLOS Biology: New Articles

  • Correction: GABAergic regulation of striatal spiny projection neurons depends upon their activity state

    by Michelle Day, Marziyeh Belal, William C. Surmeier, Alexandria Melendez, David Wokosin, Tatiana Tkatch, Vernon R. J. Clarke, D. James Surmeier



  • Prophage induction can facilitate the in vitro dispersal of multicellular <i>Streptomyces</i> structures

    by Hoda Jaffal, Mounia Kortebi, Pauline Misson, Paulo Tavares, Malika Ouldali, Hervé Leh, Sylvie Lautru, Virginia S. Lioy, François Lecointe, Stéphanie G. Bury-Moné

    Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle and play a key role in soil ecology. Little is known about the impact of Streptomyces phage on bacterial physiology. In this study, we investigated the conditions governing the expression and production of “Samy,” a prophage found in Streptomyces ambofaciens ATCC 23877. This siphoprophage is produced simultaneously with the activation of other mobile genetic elements. Remarkably, the presence and production of Samy increases bacterial dispersal under in vitro stress conditions. Altogether, this study unveiled a new property of a bacteriophage infection in the context of multicellular aggregate dynamics.

  • Alternative TSS use is widespread in <i>Cryptococcus</i> fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1

    by Thi Tuong Vi Dang, Corinne Maufrais, Jessie Colin, Frédérique Moyrand, Isabelle Mouyna, Jean-Yves COPPEE, Chinaemerem U. Onyishi, Joanna Lipecka, Ida Chiara Guerrera, Robin C. May, Guilhem Janbon

    Alternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus. We identified 2 types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (altTSS) usage genome-wide when cells switch from exponential phase to stationary phase. ChiP-Seq and DamID-Seq analyses suggest that at some loci, the role of Tur1 might be direct. Tur1 has been previously shown to be essential for virulence in C. neoformans. We demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the wild-type (WT) strain.

  • Wnt signaling modulates the response to DNA damage in the <i>Drosophila</i> wing imaginal disc by regulating the EGFR pathway

    by Ben Ewen-Campen, Norbert Perrimon

    Despite the deep conservation of the DNA damage response (DDR) pathway, cells in different contexts vary widely in their susceptibility to DNA damage and their propensity to undergo apoptosis as a result of genomic lesions. One of the cell signaling pathways implicated in modulating the DDR is the highly conserved Wnt pathway, which is known to promote resistance to DNA damage caused by ionizing radiation in a variety of human cancers. However, the mechanisms linking Wnt signal transduction to the DDR remain unclear. Here, we use a genetically encoded system in Drosophila to reliably induce consistent levels of DNA damage in vivo, and demonstrate that canonical Wnt signaling in the wing imaginal disc buffers cells against apoptosis in the face of DNA double-strand breaks. We show that Wg, the primary Wnt ligand in Drosophila, activates epidermal growth factor receptor (EGFR) signaling via the ligand-processing protease Rhomboid, which, in turn, modulates the DDR in a Chk2-, p53-, and E2F1-dependent manner. These studies provide mechanistic insight into the modulation of the DDR by the Wnt and EGFR pathways in vivo in a highly proliferative tissue. Furthermore, they reveal how the growth and patterning functions of Wnt signaling are coupled with prosurvival, antiapoptotic activities, thereby facilitating developmental robustness in the face of genomic damage.

  • “Best Paper” awards lack transparency, inclusivity, and support for Open Science

    by Malgorzata Lagisz, Joanna Rutkowska, Upama Aich, Robert M. Ross, Manuela S. Santana, Joshua Wang, Nina Trubanová, Matthew J. Page, Andrew Adrian Yu Pua, Yefeng Yang, Bawan Amin, April Robin Martinig, Adrian Barnett, Aswathi Surendran, Ju Zhang, David N. Borg, Jafsia Elisee, James G. Wrightson, Shinichi Nakagawa

    Awards can propel academic careers. They also reflect the culture and values of the scientific community. But do awards incentivize greater transparency, inclusivity, and openness in science? Our cross-disciplinary survey of 222 awards for the “best” journal articles across all 27 SCImago subject areas revealed that journals and learned societies administering such awards generally publish little detail on their procedures and criteria. Award descriptions were brief, rarely including contact details or information on the nominations pool. Nominations of underrepresented groups were not explicitly encouraged, and concepts that align with Open Science were almost absent from the assessment criteria. At the same time, 10% of awards, especially the recently established ones, tended to use article-level impact metrics. USA-affiliated researchers dominated the winner’s pool (48%), while researchers from the Global South were uncommon (11%). Sixty-one percent of individual winners were men. Overall, Best Paper awards miss the global calls for greater transparency and equitable access to academic recognition. We provide concrete and implementable recommendations for scientific awards to improve the scientific recognition system and incentives for better scientific practice.