Volume 37 Issue 7, July 2019

Clinical metagenomics on a nanopore

A scanning electron micrograph of phlegm in the trachea with bacteria shown in mauve. Charalampous et al. devise a metagenomics diagnostic method for bacterial lower respiratory tract infection that includes saponin-based host DNA depletion and nanopore long-read sequencing. Magnification: x1,500 when printed at 10cm wide.

See Charalampous et al.

Image: Steve Gschmeissner/ Science Photo Library (C038/6622). Cover Design: Erin Dewalt.

Editorial

Gene therapy’s next installment

Sky-high-priced gene therapies face slow uptake and market failure unless healthcare payers and drug makers can find common ground in ‘pay-for-performance’ reimbursement.

Editorial 02 Jul 2019

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News

‘Bubble boy’ gene therapy reignites commercial interest

Industry interest reignited by increased safety and efficacy of lentiviral gene therapies in several severe combined immune deficiencies.

Elie Dolgin
News 11 Jun 2019
First Rounders Podcast
- First Rounders: Robert Langer
  
  First Rounders Podcast 02 Jul 2019
Protein degraders, from clinic to crops

News in Brief 02 Jul 2019
Billion-dollar deal propels RNAi to CNS frontier

Biotech giant Regeneron partners with Alnylam to expand RNAi therapies beyond the liver and into the brain.

Cormac Sheridan
News 10 Jun 2019
Thrive joins liquid biopsy race

News in Brief 02 Jul 2019
Around the world in a month

News in Brief 02 Jul 2019
‘Scientific wellness’ searches for a business model

Proponents of disease prevention and wellness remain bullish, despite Arivale’s demise.

Melanie Senior
News 11 Jun 2019
Serono to pilot Nebula’s blockchain for genomes

News in Brief 02 Jul 2019

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Correspondence

Forensic genealogy and the power of defaults

Natalie Ram
Jessica L. Roberts
Correspondence 12 Jun 2019
Pre-market development times for biologic versus small-molecule drugs

Reed F. Beall
Thomas J. Hwang
Aaron S. Kesselheim
Correspondence 18 Jun 2019
A lack of evidence for six times more anxiety and depression in US graduate students than in the general population

Meghan Duffy
Carly Thanhouser
Holly Derry
Correspondence 24 Jun 2019
Reply to ‘A lack of evidence for six times more anxiety and depression in US graduate students than in the general population’

Teresa M. Evans
Lindsay Bira
Nathan L. Vanderford
Correspondence 24 Jun 2019

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Features

Public biotech 2018—the numbers

Public companies continued to ride the crest of the wave of financing, licensing deals and regulatory approvals, but clouds may be looming on the horizon for the biggest biotech players. Chris Morrison and Riku Lähteenmäki report.

Chris Morrison
Riku Lähteenmäki
Feature 21 Jun 2019
Patents
- The declining impact of the US National Institutes of Health on cancer patenting
  
  US Patent and Trademark Office data show a slowing of NIH-supported cancer patent innovation since 1995, amid criticism of an incremental rather than a high-risk, high-reward funding strategy.
  
  Raphael Zingg
  Patents 02 Jul 2019
- Synthetic biology
  
  Recent patents related to synthetic genes, microRNAs and nanoparticles.
  
  Patents 02 Jul 2019

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News & Views

Rapid diagnosis of lung infections

Nanopore sequencing of the sputum metagenome identifies respiratory pathogens in six hours.

Andrei Prodan
Morten O. A. Sommer
Max Nieuwdorp
News & Views 24 Jun 2019
CRISPR–Cas9 strikes out in cassava

Transgenic cassava expressing Cas9 is not protected from geminivirus infection.

Edward P. Rybicki
News & Views 13 Jun 2019
Cooperating on synthetic gene circuits

Ross Cloney
News & Views 02 Jul 2019

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Research

Review Articles
- Synthetic evolution
  
  From unbiased mutagenesis to precision modification, in genes or whole genomes, researchers have a panoply of tools to direct evolution.
  
  Anna J. Simon
  Simon d’Oelsnitz
  Andrew D. Ellington
  Review Article 17 Jun 2019
- Breeding crops to feed 10 billion
  
  Development of next-generation crops will be enabled by combining state-of-the-art technologies with speed breeding.
  
  Lee T. Hickey
  Amber N. Hafeez
  Brande B. H. Wulff
  Review Article 17 Jun 2019
Letters
- Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations
  
  Selective killing of bacteria in a mixed population is enabled by engineering an antimicrobial that is toxic only in pathogens harboring specific genetic elements.
  
  Rocío López-Igual
  Joaquín Bernal-Bayard
  Didier Mazel
  Letter 15 Apr 2019
- A coiled-coil masking domain for selective activation of therapeutic antibodies
  
  A general approach to mask antibodies using coiled-coil domains improves anti-tumor therapeutic efficacy.
  
  Vivian H. Trang
  Xinqun Zhang
  Matthew R. Levengood
  Letter 27 May 2019
- Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells
  
  scDamID&T combines DNA adenine methyltransferase-based labeling of protein–DNA contact sites with transcriptome sequencing to analyze regulatory programs in single cells.
  
  Koos Rooijers
  Corina M. Markodimitraki
  Jop Kind
  Letter 17 Jun 2019
Articles
- Determining cell type abundance and expression from bulk tissues with digital cytometry
  
  CIBERSORTx, a suite of computational tools, enables inference of cell type abundance and cell-type-specific gene expression profiles from bulk RNA profiles.
  
  Aaron M. Newman
  Chloé B. Steen
  Ash A. Alizadeh
  Article 06 May 2019
- Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
  
  Nanopore sequencing coupled with a metagenomics framework that effectively removes human DNA from samples enables rapid bacterial LRI diagnosis.
  
  Themoula Charalampous
  Gemma L. Kay
  Justin O’Grady
  Article 24 Jun 2019
- RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus
  
  The colocation of all RNAs in the nucleus is determined with a droplet sequencing method.
  
  Jörg Morf
  Steven W. Wingett
  Peter Fraser
  Article 01 Jul 2019
- Human 5′ UTR design and variant effect prediction from a massively parallel translation assay
  
  Ribosome loading is predictably controlled through design of 5′ UTR sequences.
  
  Paul J. Sample
  Ban Wang
  Georg Seelig
  Article 01 Jul 2019
Analysis
- A systems biology pipeline identifies regulatory networks for stem cell engineering
  
  An advanced CellNet pipeline models the dynamics of stem cell differentiation.
  
  Melissa A. Kinney
  Linda T. Vo
  George Q. Daley
  
  Collections:
  
  Harnessing the power of computational science
  
  Stem cells from development to the clinic
  Analysis 01 Jul 2019

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Amendments & Corrections

Author Correction: Brain leaks and consumer neurotechnology

Marcello Ienca
Pim Haselager
Ezekiel J. Emanuel
Author Correction 06 Jun 2019
Author Correction: A recellularized human colon model identifies cancer driver genes

Huanhuan Joyce Chen
Zhubo Wei
Michael L Shuler
Author Correction 03 Jun 2019
Author Correction: Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors

Tony P. Huang
Kevin T. Zhao
David R. Liu
Author Correction 10 Jun 2019
Publisher Correction: Biotech’s baby boom

John Hodgson
Publisher Correction 18 Jun 2019

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Careers & Recruitment

Career Feature
- Biobusiness consulting to prepare scientists for industry careers
  
  Evidence indicates that participation in a biobusiness consulting experience has an important impact on the career path of participants while not affecting their scientific productivity.
  
  Julie E. Tetzlaff
  Philip S. Clifford
  Career Feature 02 Jul 2019
People
- People
  
  A sample of goings-on in and around the biotech and pharmaceutical industry.
  
  People 02 Jul 2019

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Volume 37 Issue 7, July 2019

Clinical metagenomics on a nanopore

Editorial

News

First Rounders Podcast

Correspondence

Features

Patents

News & Views

Research

Review Articles

Letters

Articles

Analysis

Amendments & Corrections

Careers & Recruitment

Career Feature

People

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