Volume 4 Issue 5, May 2019

Volume 4 Issue 5

Pushing the envelope on viral attenuation

By combining a deep mutational scanning strategy with molecular modelling, electron microscopy as well as cellular and biochemical approaches, the authors identify key amino acids in the C-terminal domain of the Zika virus envelope protein that regulates viral replication in mosquito and human cells.

See Setoh et al.

Image: Jacob Setoh. Cover Design: Lauren Heslop.

Editorial

  • Editorial |

    Access to life-saving vaccines is still a problem for millions around the world, while others endanger public health by refusing available, safe and effective vaccines. Yet some outbreaks increasingly occur in highly vaccinated populations, highlighting the need for further vaccine development to provide long-lasting immunity.

News & Views

  • News & Views |

    Computational analysis of fungal genomes revealed that some early-branching fungi use selenocysteine, the selenium-containing amino acid, that was thought to be missing from proteins in this lineage.

    • Sergi Castellano
  • News & Views |

    Inflammatory molecules evolved partly to protect hosts from viruses, but increasing evidence suggests that they cause disease pathology and chronic conditions, and play a role in aging. By mitigating these effects, bats are able to both tolerate viral infections and live well beyond expectations.

    • David T. S. Hayman
  • News & Views |

    A large-scale comparative genomic survey of Cryptosporidium species and subtypes reveals a cryptic anthroponotic Cryptosporidium parvum branch and a large, recent superclade of species and subtypes that undergo genetic exchange, potentially facilitating host associations.

    • Jessica C. Kissinger

Correspondence

Reviews

Research

  • Analysis |

    A literature-based review evaluates host and bacterial biomarkers as well as biosignatures that may be leveraged for the diagnosis of tuberculosis.

    • Emily MacLean
    • , Tobias Broger
    • , Seda Yerlikaya
    • , B. Leticia Fernandez-Carballo
    • , Madhukar Pai
    •  & Claudia M. Denkinger
  • Letter |

    Selenoproteins—proteins that contain the twenty-first amino acid selenocysteine—were previously thought to be lacking in fungi. Analysis of genomes from early-branching fungal phyla identified selenocysteine machinery and selenoproteins, indicating that these proteins are present in all kingdoms of life.

    • Marco Mariotti
    • , Gustavo Salinas
    • , Toni Gabaldón
    •  & Vadim N. Gladyshev
  • Letter |

    Monoclonal antibody neutralization of circulating microbiota-derived peptidoglycan subunits alleviates autoimmune disease.

    • Zhenxing Huang
    • , Jianhe Wang
    • , Xiaoli Xu
    • , Haishan Wang
    • , Yuan Qiao
    • , Wern Cui Chu
    • , Shengli Xu
    • , Louis Chai
    • , Fabien Cottier
    • , Norman Pavelka
    • , Marije Oosting
    • , Leo A. B. Joosten
    • , Mihai Netea
    • , Carol Yee Leng Ng
    • , Khai Pang Leong
    • , Parag Kundu
    • , Kong-Peng Lam
    • , Sven Pettersson
    •  & Yue Wang
  • Article |

    Dampened activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome in bat primary immune cells in response to infection with multiple zoonotic viruses is caused by decreased transcriptional priming, the presence of a unique splice variant and an altered leucine-rich repeat domain of bat NLRP3.

    • Matae Ahn
    • , Danielle E. Anderson
    • , Qian Zhang
    • , Chee Wah Tan
    • , Beng Lee Lim
    • , Katarina Luko
    • , Ming Wen
    • , Wan Ni Chia
    • , Shailendra Mani
    • , Loo Chien Wang
    • , Justin Han Jia Ng
    • , Radoslaw M. Sobota
    • , Charles-Antoine Dutertre
    • , Florent Ginhoux
    • , Zheng-Li Shi
    • , Aaron T. Irving
    •  & Lin-Fa Wang
  • Article |

    NOD-like receptor family pyrin domain-containing 6 (NLRP6) reduces colitis severity in a gut microbiome-dependent manner; however, in the context of murine intestinal graft-versus-host disease, NLRP6 exacerbates symptoms independently of gut microbiome composition and diversity, with NLRP6-deficient animals displaying protection against disease.

    • Tomomi Toubai
    • , Hideaki Fujiwara
    • , Corinne Rossi
    • , Mary Riwes
    • , Hiroya Tamaki
    • , Cynthia Zajac
    • , Chen Liu
    • , Anna V. Mathew
    • , Jaeman Byun
    • , Katherine Oravecz-Wilson
    • , Ikuo Matsuda
    • , Yaping Sun
    • , Daniel Peltier
    • , Julia Wu
    • , Jiachen Chen
    • , Sergey Seregin
    • , Israel Henig
    • , Stephanie Kim
    • , Stuart Brabbs
    • , Subramaniam Pennathur
    • , Grace Chen
    •  & Pavan Reddy
  • Article |

    Proteomic analysis of human immunodeficiency virus (HIV-1)-infected human primary T cells identifies P-selectin glycoprotein ligand 1 as an HIV-1 restriction factor, which can inhibit HIV-1 reverse transcription and block viral infectivity through incorporation in progeny virions antagonized by HIV-1 viral protein U.

    • Ying Liu
    • , Yajing Fu
    • , Qian Wang
    • , Mushan Li
    • , Zheng Zhou
    • , Deemah Dabbagh
    • , Chunyan Fu
    • , Hang Zhang
    • , Shuo Li
    • , Tengjiang Zhang
    • , Jing Gong
    • , Xiaohui Kong
    • , Weiwei Zhai
    • , Jiaming Su
    • , Jianping Sun
    • , Yonghong Zhang
    • , Xiao-Fang Yu
    • , Zhen Shao
    • , Feng Zhou
    • , Yuntao Wu
    •  & Xu Tan
  • Article |

    A comparative analysis of Cryptosporidium genome sequences elucidates the evolutionary history of these parasites and highlights changes associated with its human adaptation.

    • Johanna L. Nader
    • , Thomas C. Mathers
    • , Ben J. Ward
    • , Justin A. Pachebat
    • , Martin T. Swain
    • , Guy Robinson
    • , Rachel M. Chalmers
    • , Paul R. Hunter
    • , Cock van Oosterhout
    •  & Kevin M. Tyler
  • Article |

    Near-atomic resolution structure of bluetongue virus non-structural protein 1 (NS1) provides insights into its dynamic tubular assemblies and their contribution to NS1 function in viral protein synthesis.

    • Adeline Kerviel
    • , Peng Ge
    • , Mason Lai
    • , Jonathan Jih
    • , Mark Boyce
    • , Xing Zhang
    • , Z. Hong Zhou
    •  & Polly Roy
  • Article |

    A trait-based approach used to quantify the niches of 23 species of saprotrophic wood decomposer fungi collected throughout North America provides preliminary insight into the linkages among functional trait expression, climate and phylogeny.

    • Daniel S. Maynard
    • , Mark A. Bradford
    • , Kristofer R. Covey
    • , Daniel Lindner
    • , Jessie Glaeser
    • , Douglas A. Talbert
    • , Paul Joshua Tinker
    • , Donald M. Walker
    •  & Thomas W. Crowther
  • Article | | Open Access

    Statistical mapping techniques provide insights into the spread of two key arbovirus vectors in Europe and the United States, and predict the future distributions of both mosquitoes in response to accelerating urbanization, connectivity and climate change.

    • Moritz U. G. Kraemer
    • , Robert C. Reiner Jr
    • , Oliver J. Brady
    • , Jane P. Messina
    • , Marius Gilbert
    • , David M. Pigott
    • , Dingdong Yi
    • , Kimberly Johnson
    • , Lucas Earl
    • , Laurie B. Marczak
    • , Shreya Shirude
    • , Nicole Davis Weaver
    • , Donal Bisanzio
    • , T. Alex Perkins
    • , Shengjie Lai
    • , Xin Lu
    • , Peter Jones
    • , Giovanini E. Coelho
    • , Roberta G. Carvalho
    • , Wim Van Bortel
    • , Cedric Marsboom
    • , Guy Hendrickx
    • , Francis Schaffner
    • , Chester G. Moore
    • , Heinrich H. Nax
    • , Linus Bengtsson
    • , Erik Wetter
    • , Andrew J. Tatem
    • , John S. Brownstein
    • , David L. Smith
    • , Louis Lambrechts
    • , Simon Cauchemez
    • , Catherine Linard
    • , Nuno R. Faria
    • , Oliver G. Pybus
    • , Thomas W. Scott
    • , Qiyong Liu
    • , Hongjie Yu
    • , G. R. William Wint
    • , Simon I. Hay
    •  & Nick Golding
  • Article |

    Using integrated metagenomics, metaproteomics and metabolomics approaches, the authors characterize the microbial taxa and metabolic pathways facilitating lignocellulose degradation across gut compartments of a wood-feeding beetle.

    • Javier A. Ceja-Navarro
    • , Ulas Karaoz
    • , Markus Bill
    • , Zhao Hao
    • , Richard A. White III
    • , Abelardo Arellano
    • , Leila Ramanculova
    • , Timothy R. Filley
    • , Timothy D. Berry
    • , Mark E. Conrad
    • , Meredith Blackwell
    • , Carrie D. Nicora
    • , Young-Mo Kim
    • , Patrick N. Reardon
    • , Mary S. Lipton
    • , Joshua N. Adkins
    • , Jennifer Pett-Ridge
    •  & Eoin L. Brodie
  • Article |

    By combining a deep mutational scanning strategy with molecular modelling, electron microscopy as well as cellular and biochemical approaches, the authors identify key amino acids in the C-terminal domain of the Zika virus envelope protein (E) that regulate viral replication in mosquito and human cells.

    • Yin Xiang Setoh
    • , Alberto A. Amarilla
    • , Nias Y. G. Peng
    • , Rebecca E. Griffiths
    • , Julio Carrera
    • , Morgan E. Freney
    • , Eri Nakayama
    • , Shinya Ogawa
    • , Daniel Watterson
    • , Naphak Modhiran
    • , Faith Elizabeth Nanyonga
    • , Francisco J. Torres
    • , Andrii Slonchak
    • , Parthiban Periasamy
    • , Natalie A. Prow
    • , Bing Tang
    • , Jessica Harrison
    • , Jody Hobson-Peters
    • , Thom Cuddihy
    • , Justin Cooper-White
    • , Roy A. Hall
    • , Paul R. Young
    • , Jason M. Mackenzie
    • , Ernst Wolvetang
    • , Jesse D. Bloom
    • , Andreas Suhrbier
    •  & Alexander A. Khromykh

Amendments & Corrections

  • Author Correction |

    • Eric A. Franzosa
    • , Alexandra Sirota-Madi
    • , Julian Avila-Pacheco
    • , Nadine Fornelos
    • , Henry J. Haiser
    • , Stefan Reinker
    • , Tommi Vatanen
    • , A. Brantley Hall
    • , Himel Mallick
    • , Lauren J. McIver
    • , Jenny S. Sauk
    • , Robin G. Wilson
    • , Betsy W. Stevens
    • , Justin M. Scott
    • , Kerry Pierce
    • , Amy A. Deik
    • , Kevin Bullock
    • , Floris Imhann
    • , Jeffrey A. Porter
    • , Alexandra Zhernakova
    • , Jingyuan Fu
    • , Rinse K. Weersma
    • , Cisca Wijmenga
    • , Clary B. Clish
    • , Hera Vlamakis
    • , Curtis Huttenhower
    •  & Ramnik J. Xavier
  • Publisher Correction |

    • Moritz U. G. Kraemer
    • , Robert C. Reiner Jr
    • , Oliver J. Brady
    • , Jane P. Messina
    • , Marius Gilbert
    • , David M. Pigott
    • , Dingdong Yi
    • , Kimberly Johnson
    • , Lucas Earl
    • , Laurie B. Marczak
    • , Shreya Shirude
    • , Nicole Davis Weaver
    • , Donal Bisanzio
    • , T. Alex Perkins
    • , Shengjie Lai
    • , Xin Lu
    • , Peter Jones
    • , Giovanini E. Coelho
    • , Roberta G. Carvalho
    • , Wim Van Bortel
    • , Cedric Marsboom
    • , Guy Hendrickx
    • , Francis Schaffner
    • , Chester G. Moore
    • , Heinrich H. Nax
    • , Linus Bengtsson
    • , Erik Wetter
    • , Andrew J. Tatem
    • , John S. Brownstein
    • , David L. Smith
    • , Louis Lambrechts
    • , Simon Cauchemez
    • , Catherine Linard
    • , Nuno R. Faria
    • , Oliver G. Pybus
    • , Thomas W. Scott
    • , Qiyong Liu
    • , Hongjie Yu
    • , G. R. William Wint
    • , Simon I. Hay
    •  & Nick Golding
  • Publisher Correction | | Open Access

    • Moritz U. G. Kraemer
    • , Robert C. Reiner Jr
    • , Oliver J. Brady
    • , Jane P. Messina
    • , Marius Gilbert
    • , David M. Pigott
    • , Dingdong Yi
    • , Kimberly Johnson
    • , Lucas Earl
    • , Laurie B. Marczak
    • , Shreya Shirude
    • , Nicole Davis Weaver
    • , Donal Bisanzio
    • , T. Alex Perkins
    • , Shengjie Lai
    • , Xin Lu
    • , Peter Jones
    • , Giovanini E. Coelho
    • , Roberta G. Carvalho
    • , Wim Van Bortel
    • , Cedric Marsboom
    • , Guy Hendrickx
    • , Francis Schaffner
    • , Chester G. Moore
    • , Heinrich H. Nax
    • , Linus Bengtsson
    • , Erik Wetter
    • , Andrew J. Tatem
    • , John S. Brownstein
    • , David L. Smith
    • , Louis Lambrechts
    • , Simon Cauchemez
    • , Catherine Linard
    • , Nuno R. Faria
    • , Oliver G. Pybus
    • , Thomas W. Scott
    • , Qiyong Liu
    • , Hongjie Yu
    • , G. R. William Wint
    • , Simon I. Hay
    •  & Nick Golding