Papers Aloud: Recent Episodes
Arkadiy Garber
This podcasts features readings of open-access (CC BY) primary research articles and reviews relevant to evolutionary and cell biology, environmental and clinical microbiology, symbiosis, geobiology, and bioinformatics.
I avoid Methods sections, and sometimes Results (depending on how amenable it is to reading out loud). Abstract, Introduction, Discussion, and Conclusions are always included.
If you are an author of a research article and would like to have your work converted to an audio format, or send me an audio recording of your paper, please reach out to rkdgarber@gmail.edu.
Title: A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
Authors: Pengyao Jiang, Anja R Ollodart, Vidha Sudhesh, Alan J Herr, Maitreya J Dunham, Kelley Harris
Citation: Jiang, P., Ollodart, A. R., Sudhesh, V., Herr, A. J., Dunham, M. J., & Harris, K. (2021). A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae. eLife, 10. https://doi.org/10.7554/eLife.68285.
Link to article
Title: Molecular Evolutionary Dynamics of Energy Limited Microorganisms
Authors: William R. Shoemaker, Evgeniya Polezhaeva, Kenzie B. Givens, and Jay T. Lennon
Citation: Shoemaker, W. R., Polezhaeva, E., Givens, K. B., & Lennon, J. T. (2021). Molecular Evolutionary Dynamics of Energy Limited Microorganisms. Molecular Biology and Evolution, 38(10), 4532–4545.
Link to article
Title: The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation
Authors: Jin-Der Wen, Syue-Ting Kuo, and Hsin-Hung David Chou.
Citation: Wen, J.-D., Kuo, S.-T., & Chou, H.-H. D. (2021). The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biology, 18(11), 1489–1500.
Link to article
Title: Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont
Authors: Taras Y. Nechitaylo, Mario Sandoval-Calderónb\, Tobias Engl, Natalie Wielsch, Diane M. Dunne, Alexander Goesmann, Erhard Strohm, Aleš Svatoš, Colin Dale, Robert B. Weiss, and Martin Kaltenpoth
Citation: Nechitaylo, T. Y., Sandoval-Calderón, M., Engl, T., Wielsch, N., Dunn, D. M., Goesmann, A., Strohm, E., Svatoš, A., Dale, C., Weiss, R. B., & Kaltenpoth, M. (2021). Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont. Proceedings of the National Academy of Sciences of the United States of America, 118(17). https://doi.org/10.1073/pnas.2023047118
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defensive symbiosis|protective mutualism|genome erosion|pseudogenization|Streptomyces
Title: Pervasive translation in Mycobacterium tuberculosis
Authors: Carol Smith, Jill G Canestrari, Archer J Wang, Matthew M Champion, Keith M Derbyshire, Todd A Gray, Joseph T Wade.
Citation: Smith, C., Canestrari, J. G., Wang, A. J., Champion, M. M., Derbyshire, K. M., Gray, T. A., & Wade, J. T. (2022). Pervasive translation in Mycobacterium tuberculosis. eLife, 11. https://doi.org/10.7554/eLife.73980
Link to article
Simonsen, A. K. (2021). Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria. The ISME Journal. https://doi.org/10.1038/s41396-021-01082-x
Title: Environmental stress leads to genome streamlining in a widely
distributed species of soil bacteria
Authors: Anna K. Simonsen
Citation: Simonsen, A. K. (2021). Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria. The ISME Journal. https://doi.org/10.1038/s41396-021-01082-x
Link to article
Title: Are Aliens among Us
Authors: Paul Davies
Citation: Davies, P. (2007). Are Aliens among Us? Scientific American, 297(6), 62–69.
Link to article
Title: Environmental stress leads to genome streamlining in a widely
distributed species of soil bacteria
Authors: Anna K. Simonsen
Citation: Simonsen, A. K. (2021). Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria. The ISME Journal. https://doi.org/10.1038/s41396-021-01082-x
Link to article
Title: Principles of Geobiochemistry
Authors: Everett L. Shock and Eric S. Boyd
Citation: Shock, E. L., & Boyd, E. S. (2015). Principles of Geobiochemistry. Elements , 11(6), 395–401.
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Title: The imitation game—a computational chemical approach to recognizing life
Authors: Leroy Cronin, Natalio Krasnogor, Benjamin G Davis, Cameron Alexander, Neil Robertson, Joachim H G Steinke, Sven L M Schroeder, Andrei N Khlobystov, Geoff Cooper, Paul M Gardner, Peter Siepmann, Benjamin J Whitaker & Dan Marsh
Citation: Cronin, L., Krasnogor, N., Davis, B. G., Alexander, C., Robertson, N., Steinke, J. H. G., Schroeder, S. L. M., Khlobystov, A. N., Cooper, G., Gardner, P. M., Siepmann, P., Whitaker, B. J., & Marsh, D. (2006). The imitation game--a computational chemical approach to recognizing life. Nature Biotechnology, 24(10), 1203–1206.
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Title: Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment
Authors: William D. Orsi, Tobias Magritsch, Sergio Vargas, Ömer K. Coskun, Aurele Vuillemin, Sebastian Höhna, Gert Wörheide, Steven D’Hondt, B. Jesse Shapiro, Paul Carini
Citation: Orsi, W. D., Magritsch, T., Vargas, S., Coskun, Ö. K., Vuillemin, A., Höhna, S., Wörheide, G., D’Hondt, S., Shapiro, B. J., & Carini, P. (2021). Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment. mBio, 12(4), e0115021.
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Title: The Multiple Paths to Multiple Life
Authors: Christopher P. Kempes and David C. Krakauer
Citation: Kempes, C. P., & Krakauer, D. C. (2021). The Multiple Paths to Multiple Life. Journal of Molecular Evolution, 89(7), 415–426.
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Title: Genetic innovations in animal–microbe symbioses
Authors: Julie Perreau and Nancy A. Moran
Citation: Perreau, J., & Moran, N. A. (2021). Genetic innovations in animal-microbe symbioses. Nature Reviews. Genetics. https://doi.org/10.1038/s41576-021-00395-z
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Title: Discovery of a Diverse Set of Bacteria That Build Their Cell Walls without the Canonical Peptidoglycan Polymerase aPBP.
Authors: Sharanjeet Atwal, Suthida Chuenklin, Edward M. Bonder, Juan Flores, Joseph J. Gillespie, Timothy P. Driscoll, Jeanne Salje.
Citation: Atwal, S., Chuenklin, S., Bonder, E. M., Flores, J., Gillespie, J. J., Driscoll, T. P., & Salje, J. (n.d.). Discovery of a Diverse Set of Bacteria That Build Their Cell Walls without the Canonical Peptidoglycan Polymerase aPBP. https://doi.org/10.1128/mBio.01342-21.
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Title: Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont.
Authors: Ian Goodhead, Frances Blow, Philip Brownridge, Margaret Hughes, John Kenny, Ritesh Krishna, Lynn McLean, Pisut Pongchaikul, Rob Beynon, and Alistair C. Darby.
Citation: Goodhead, I., Blow, F., Brownridge, P., Hughes, M., Kenny, J., Krishna, R., McLean, L., Pongchaikul, P., Beynon, R., & Darby, A. C. (2020). Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microbial Genomics, 6(1). https://doi.org/10.1099/mgen.0.000285.
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Title: Rapid compensatory evolution can rescue low fitness symbioses following partner switching.
Authors: Megan E.S. Sørensen, A. Jamie Wood, Duncan D. Cameron, Michael A. Brockhurst.
Citation: Sørensen,M.E.S. et al. (2021) Rapid compensatory evolution can rescue low fitness symbioses following partner switching. Curr. Biol..
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Title: At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica.
Authors: François Renoz, Vincent Foray, Jérôme Ambroise, Patrice Baa-Puyoulet, Bertrand Bearzatto, Gipsi Lima Mendez, Alina S. Grigorescu, Jacques Mahillon, Patrick Mardulyn, Jean-Luc Gala, Federica Calevro, and Thierry Hance.
Citation: Renoz, F. et al. (2021) At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. Front. Cell. Infect. Microbiol., 11, 660007.
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Title: Borgs are giant extrachromosomal elements with the potential to augment methane oxidation.
Authors: Basem Al-Shayeb, Marie C. Schoelmerich, Jacob West-Roberts, Luis E. Valentin-Alvarado, Rohan Sachdeva, Susan Mullen, Alexander Crits-Christoph, Michael J. Wilkins, Kenneth H. Williams, Jennifer A. Doudna, Jillian F. Banfield.
Citation: Al-Shayeb, B. et al. (2021) Borgs are giant extrachromosomal elements with the potential to augment methane oxidation. bioRxiv, 2021.07.10.451761.
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Title: Bacterial and archaeal symbioses with protists.
Authors: Filip Husnik, Daria Tashyreva, Vittorio Boscaro, Emma E. George, Julius Lukes, and Patrick J. Keeling.
Citation: Husnik,F. et al. (2021) Bacterial and archaeal symbioses with protists. Curr. Biol., 31, R862–R877.
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Title: Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae.
Authors: Clarisse Uwizeye, Margaret Mars Brisbin, Benoit Gallet, Fabien Chevalier, Charlotte LeKieffre, Nicole L. Schieber, Denis Falconet, Daniel Wangpraseurt, Lukas Schertel, Hryhoriy Stryhanyuk, Niculina Musat, Satoshi Mitarai, Yannick Schwab, Giovanni Finazzi, and Johan Decelle.
Citation: Uwizeye,C. et al. (2021) Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae. Proc. Natl. Acad. Sci. U. S. A., 118.
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Title: Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes.
Authors: Gulnara Tagirdzhanova, Paul Saary, Jeffrey P. Tingley, David Dıaz-Escando, D. Wade Abbott, Robert D. Finn2 and Toby Spribille.
Citation: Tagirdzhanova, G. et al. (2021) Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. Genome Biol. Evol., 13.
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Title: Natural selection shapes maintenance of orthologous sRNAs in divergent host-restricted bacterial genomes.
Authors: Margaret W. Thairu, Venkata Rama Sravani Meduri, Patrick H. Degnan, Allison K. Hansen.
Citation: Thairu, M.W. et al. (2021) Natural selection shapes maintenance of orthologous sRNAs in divergent host-restricted bacterial genomes. Mol. Biol. Evol.
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Title: Evidence of streamlined extracellular electron transfer pathway from biofilm structure, metabolic stratification, and long-range electron transfer parameters.
Authors: Fernanda Jiménez Otero, Grayson L. Chadwick, Matthew D. Yates, Rebecca L. Mickol, Scott H. Saunders, Sarah M. Glaven, Jeffrey A. Gralnick, Dianne K. Newman, Leonard M. Tender, Victoria J. Orphan, Daniel R. Bond.
Citation: Jiménez Otero, F. et al. (2021) Evidence of streamlined extracellular electron transfer pathway from biofilm structure, metabolic stratification, and long-range electron transfer parameters. Appl. Environ. Microbiol., AEM0070621.
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Title: Modeling host-associating microbes under selection
Authors: Florence Bansept, Nancy Obeng, Hinrich Schulenburg, and Arne Traulsen
Citation: Bansept, F. et al. (2021) Modeling host-associating microbes under selection. ISME J.
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Title: Reconstruction of ancient microbial genomes from the human gut
Authors: Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Hübner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto García-Ortiz, Angélica Martínez-Hernández, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Sünje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, and Aleksandar D. Kostic
Citation: Wibowo, M.C. et al. (2021) Reconstruction of ancient microbial genomes from the human gut. Nature, 594, 234–239.
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Title: The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements
Authors: Tomasz Zajkowski, Michael D. Lee, Shamba S. Mondal, Amanda Carbajal, Robert Dec, Patrick D. Brennock, Radoslaw W. Piast, Jessica E. Snyder, Nicholas B. Bense, Wojciech Dzwolak, Daniel F. Jarosz, and Lynn J. Rothschild
Citation: Zajkowski, T. et al. (2021) The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. Mol. Biol. Evol., 38, 2088–2103.
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Title: Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp.
Authors: Tomáš Skalický, João M. P. Alves , Anderson C. Morais, Jana Režnarová, Anzhelika Butenko, Julius Lukeš, Myrna G. Serrano, Gregory A. Buck, Marta M. G. Teixeira, Erney P. Camargo, Mandy Sanders, James A. Cotton, Vyacheslav Yurchenko, and Alexei Y. Kostygov
Citation: Skalický,T. et al. (2021) Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp. Pathogens, 10, 702.
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Title: Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood
Authors: Vojtēch Tláskal, Victor Satler Pylro, Lucia Žifčáková, and Petr Baldrian
Citation: Tláskal,V. et al. (2021) Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood. Front. Microbiol., 12, 1499.
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Title: A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts
Authors: Sergio A. Muñoz-Gómez, Martin Kreutz, Sebastian Hess
Citation: Muñoz-Gómez, S.A. et al. (2021) A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts. Sci Adv, 7.
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Title: Survival of the first rather than the fittest in a Shewanella electrode biofilm
Authors: Eric D. Kees, Caleb E. Levar, Stephen P. Miller, Daniel R. Bond, Jeffrey A. Gralnick, and Antony M. Dean
Citation: Kees, E.D. et al. (2021) Survival of the first rather than the fittest in a Shewanella electrode biofilm. Commun Biol, 4, 536.
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Title: Ecology and molecular targets of hypermutation in the global microbiome
Authors: Simon Roux , Blair G. Paul, Sarah C. Bagby, Stephen Nayfach, Michelle A. Allen, Graeme Attwood, Ricardo Cavicchioli, Ludmila Chistoserdova, Robert J. Gruninger, Steven J. Hallam, Maria E. Hernandez, Matthias Hess, Wen-Tso Liu, Tim A. McAllister, Michelle A. O’Malley, Xuefeng Peng, Virginia I. Rich, Scott R. Saleska, and Emiley A. Eloe-Fadrosh
Citation: Roux, S. et al. (2021) Ecology and molecular targets of hypermutation in the global microbiome. Nat. Commun., 12, 3076.
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Title: Transposable elements drive the evolution of genome streamlining
Authors: Bram van Dijk, Frederic Bertels, Lianne Stolk, Nobuto Takeuchi, and Paul B. Rainey
Citation: van Dijk, B. et al. (2021) Transposable elements drive the evolution of genome streamlining. bioRxiv, 2021.05.29.446280.
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Title: Dinoflagellate symbionts escape vomocytosis by host cell immune suppression
Authors: Marie R. Jacobovitz, Sebastian Rupp, Philipp A. Voss, Ira Maegele, Sebastian G. Gornik, and Annika Guse
Citation: Jacobovitz, M.R. et al. (2021) Dinoflagellate symbionts escape vomocytosis by host cell immune suppression. Nature Microbiology, 6, 769–782.
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Title: A Dynamic Interface between Vacuoles and Mitochondria in Yeast.
Authors: Yael Elbaz-Alon, Eden Rosenfeld-Gur, Vera Shinder, Anthony H. Futerman, Tamar Geiger, and Maya Schuldiner.
Citation: Elbaz-Alon, Y. et al. (2014) A dynamic interface between vacuoles and mitochondria in yeast. Dev. Cell, 30, 95–102.
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Title: Engineering yeast endosymbionts as a step toward the evolution of mitochondria
Authors: Angad P. Mehta, Lubica Supekova, Jian-Hua Chen, Kersi Pestonjamasp, Paul Webster, Yeonjin Ko, Scott C. Henderson, Gerry McDermott, Frantisek Supeke, and Peter G. Schultz
Citation: Mehta,A.P. et al. (2018) Engineering yeast endosymbionts as a step toward the evolution of mitochondria. Proc. Natl. Acad. Sci. U. S. A., 115, 11796–11801.
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Title: A novel symbiosis between chemoautotrophic bacteria and a freshwater cave amphipod
Authors: Sharmishtha Dattagupta, Irene Schaperdoth, Alessandro Montanari, Sandro Mariani, Noriko Kita, John W Valley, and Jennifer L Macalady
Citation: Dattagupta, S. et al. (2009) A novel symbiosis between chemoautotrophic bacteria and a freshwater cave amphipod. ISME J., 3, 935–943.
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Title: Metabolic Integration of Bacterial Endosymbionts through Antimicrobial Peptides
Authors: Peter Mergaert, Yoshitomo Kikuchi, Shuji Shigenobu, and Eva C.M. Nowack
Citation: Mergaert, P. et al. (2017) Metabolic Integration of Bacterial Endosymbionts through Antimicrobial Peptides. Trends Microbiol., 25, 703–712.
Link to article
Title: Horizontal genome transfer by cell-to-cell travel of whole organelles.
Authors: Alexander P. Hertle, Benedikt Haberl, Ralph Bock.
Citation: Hertle, A.P. et al. (2021) Horizontal genome transfer by cell-to-cell travel of whole organelles. Science Advances, 7, eabd8215.
Link to Article: https://advances.sciencemag.org/content/7/1/eabd8215
Title: The Origin and Diversification of Mitochondria.
Authors: Andrew J. Roger, Sergio A. Muñoz-Gómez, and Ryoma Kamikawa.
Citation: Roger,A.J. et al. (2017) The Origin and Diversification of Mitochondria. Curr. Biol., 27, R1177–R1192.
Link to article: https://www.cell.com/action/showPdf?pii=S0960-9822%2817%2931179-X
Title: Ten common statistical mistakes to watch out for when writing or reviewing a manuscript.
Authors: Tamar R. Markin and Jean-Jacques Orban de Xivry.
Citation: Makin,T.R. and Orban de Xivry,J.-J. (2019) Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. Elife, 8, e48175.
Link to article: https://elifesciences.org/articles/48175
Title: Simplification of Ribosomes in Bacteria with Tiny Genomes.
Authors: Daria D. Nikolaeva, Mikhail S. Gelfand, and Sofya K. Garushyants.
Citation: Nikolaeva, D.D. et al. (2021) Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol. Biol. Evol., 38, 58–66.
Link: https://academic.oup.com/mbe/article/38/1/58/5873528
Title: Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence.
Authors: Gemma G.R. Murray, Jane Charlesworth, Eric L. Miller, Michael J. Casey, Catrin T. Lloyd, Marcelo Gottschalk, Alexander W. (Dan) Tucker, John J. Welch, and Lucy A. Weinert.
Citation: Murray, G.G.R. et al. (2021) Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence. Mol. Biol. Evol., 38, 1570–1579.
Link: https://academic.oup.com/mbe/article/38/4/1570/6031917
Title: Coordination of host and symbiont gene expression reveals a metabolic tug-of-war between aphids and Buchnera
Authors: Thomas E. Smith and Nancy A. Moran
Citation: Smith, T.E. and Moran,N.A. (2020) Coordination of host and symbiont gene expression reveals a metabolic tug-of-war between aphids and Buchnera. Proc. Natl. Acad. Sci. U. S. A., 117, 2113–2121.
Link to article: https://www.pnas.org/content/117/4/2113
Title: Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora.
Authors: Eva C. M. Nowacka, Dana C. Price, Debashish Bhattacharya, Anna Singer, Michael Melkonian, and Arthur R. Grossman.
Citation: Nowack, E.C.M. et al. (2016) Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora. Proc. Natl. Acad. Sci. U. S. A., 113, 12214–12219.
Link to article: https://www.pnas.org/content/113/43/12214