Nature Biotechnology 31, 365 (2013). doi:10.1038/nbt.2587

Judicious choice of a target tumor antigen for adoptive T-cell therapy remains crucial not only for efficacy but also for avoiding serious toxicities.

Nature Biotechnology and other Nature journals are updating editorial policies with the aim of improving transparency and reproducibility.

Author: Ken Garber

A University of California, San Francisco, startup offers a reversible twist on covalent drugs.

Author: Jeffrey L Fox

Better understanding of the mechanisms of action, modification and synthesis of antimicrobial peptides is reigniting commercial development. Jeffrey L. Fox reports.

Authors: Lynda Chin, Frederic de Sauvage, Mikala Egeblad, Kenneth P Olive, David Tuveson & William Weiss

A panel of experts discusses the challenge of translating findings from current mouse models to the clinic.

Author: Brady Huggett

Academic tech transfer keeps on spinning out startups, but the pool of capital to sustain such ventures is dwindling.

Authors: Gregory D Graff, Devon Phillips, Zhen Lei, Sooyoung Oh, Carol Nottenburg & Philip G Pardey

A new study assesses the impact of recent US Supreme Court rulings on the changing landscape of US patents claiming nucleic acids.

Author: Steven A Goldman

Myelinating oligodendrocytes are induced from murine embryonic fibroblasts by transcription factor–mediated reprogramming.

Authors: Andre C Maranhao & Andrew D Ellington

Genetic circuits that process and permanently store information are created with recombinases that flip the orientation of DNA cassettes.

Author: Ferric C Fang

New work fuels the controversy over the role of reactive oxygen species (ROS) in the activity of bactericidal antibiotics.

Authors: Christopher M Sturgeon, Andrea Ditadi, Raedun L Clarke & Gordon Keller

New insights into hemogenic endothelium will facilitate efforts to produce hematopoietic stem cells in vitro.

Authors: Ines Thiele, Neil Swainston, Ronan M T Fleming, Andreas Hoppe, Swagatika Sahoo, Maike K Aurich, Hulda Haraldsdottir, Monica L Mo, Ottar Rolfsson, Miranda D Stobbe, Stefan G Thorleifsson, Rasmus Agren, Christian Bölling, Sergio Bordel, Arvind K Chavali, Paul Dobson, Warwick B Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon J Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le Novère, Naglis Malys, Alexander Mazein, Jason A Papin, Nathan D Price, Evgeni Selkov, Martin I Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes H G M van Beek, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans V Westerhoff, Douglas B Kell, Pedro Mendes & Bernhard Ø Palsson

Authors: Fadi J Najm, Angela M Lager, Anita Zaremba, Krysta Wyatt, Andrew V Caprariello, Daniel C Factor, Robert T Karl, Tadao Maeda, Robert H Miller & Paul J Tesar

Authors: Nan Yang, J Bradley Zuchero, Henrik Ahlenius, Samuele Marro, Yi Han Ng, Thomas Vierbuchen, John S Hawkins, Richard Geissler, Ben A Barres & Marius Wernig

Authors: Yan Liu, Jason P Weick, Huisheng Liu, Robert Krencik, Xiaoqing Zhang, Lixiang Ma, Guo-min Zhou, Melvin Ayala & Su-Chun Zhang

Authors: Piro Siuti, John Yazbek & Timothy K Lu

Logic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications.

Authors: Michiko Kimoto, Rie Yamashige, Ken-ichiro Matsunaga, Shigeyuki Yokoyama & Ichiro Hirao

DNA aptamers produced with natural or modified natural nucleotides often lack the desired binding affinity and specificity to target proteins. Here we describe a method for selecting DNA aptamers containing the four natural nucleotides and an unnatural nucleotide with the hydrophobic base 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds). We incorporated up to three Ds nucleotides in a random sequence library, which is expected to increase the chemical and structural diversity of the DNA molecules. Selection experiments against two human target proteins, vascular endothelial cell growth factor-165 (VEGF-165) and interferon-γ (IFN-γ), yielded DNA aptamers that bind with KD values of 0.65 pM and 0.038 nM, respectively, affinities that are >100-fold improved over those of aptamers containing only natural bases. These results show that incorporation of unnatural bases can yield aptamers with greatly augmented affinities, suggesting the potential of genetic alphabet expansion as a powerful tool for creating highly functional nucleic acids.

Authors: Vahid Khoddami & Bradley R Cairns

The extent and biological impact of RNA cytosine methylation are poorly understood, in part owing to limitations of current techniques for determining the targets of RNA methyltransferases. Here we describe 5-azacytidine–mediated RNA immunoprecipitation (Aza-IP), a technique that exploits the covalent bond formed between an RNA methyltransferase and the cytidine analog 5-azacytidine to recover RNA targets by immunoprecipitation. Targets are subsequently identified by high-throughput sequencing. When applied in a human cell line to the RNA methyltransferases DNMT2 and NSUN2, Aza-IP enabled >200-fold enrichment of tRNAs that are known targets of the enzymes. In addition, it revealed many tRNA and noncoding RNA targets not previously associated with NSUN2. Notably, we observed a high frequency of C→G transversions at the cytosine residues targeted by both enzymes, allowing identification of the specific methylated cytosine(s) in target RNAs. Given the mechanistic similarity of RNA cytosine methyltransferases, Aza-IP may be generally applicable for target identification.