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| Open AccessDefining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling
Protein phosphorylation is known to play an important role in cell adhesion signalling. Robertson et al. present a proteomic resource mapping the phosphorylation states of proteins isolated from adhesion complexes and, taking advantage of this data set, show that the cell cycle kinase CDK1 may influence cell adhesion.
- Joseph Robertson
- , Guillaume Jacquemet
- & Martin J. Humphries
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Article
| Open AccessMechanism of erosion of nanostructured porous silicon drug carriers in neoplastic tissues
The degradation of materials used in biological applications has an important bearing on their long term performance. Here, the authors show how porous silicon nanoparticle degradation can be accelerated in vivothrough the influence of local tissue pathology, likely influencing drug delivery performance.
- Adi Tzur-Balter
- , Zohar Shatsberg
- & Natalie Artzi
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Off-target-free gene delivery by affinity-purified receptor-targeted viral vectors
The clinical use of adeno-associated virus vectors (AAVs) has been limited by the lack of transduction specificity. Here the authors show that receptor-targeted, affinity-tagged, and purified AVVs reach tumours in mouse models with high selectivity and efficiency, outperforming therapeutic antibodies.
- Robert C. Münch
- , Anke Muth
- & Christian J. Buchholz
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Sulphur shuttling across a chaperone during molybdenum cofactor maturation
Microbial formate dehydrogenases (FDH) are molybdenum-containing enzymes that can catalyse the reduction of CO2 into formate. Here, the authors suggest a structural and functional basis for sulphuration of the molybdenum cofactor in E. coliFDH, a key step in the production of active formate dehydrogenase.
- Pascal Arnoux
- , Christian Ruppelt
- & Anne Walburger
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Article
| Open AccessGd-metallofullerenol nanomaterial as non-toxic breast cancer stem cell-specific inhibitor
A metallofullerenol nanomaterial, Gd@C82(OH)22, was shown to inhibit growth of several solid cancers in preclinical models and yet exhibit low toxicity. Herein the authors show that Gd@C82(OH)22functions as an inhibitor of breast cancer stem cell function via blocking TGF-β and HIF-1α signalling, while sparing normal tissue.
- Ying Liu
- , Chunying Chen
- & Yuliang Zhao
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Article
| Open AccessGene therapy restores vision in rd1 mice after removal of a confounding mutation in Gpr179
The rd1 mouse is the most widely used model to study retinal degeneration. Here, the authors identify a wide-spread mutation in these mice that may explain the failure of previous gene therapeutic approaches and show that long-lasting restoration of vision is possible in rd1 mice without this mutation.
- Koji M. Nishiguchi
- , Livia S. Carvalho
- & Robin R. Ali
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PD-L1hi B cells are critical regulators of humoral immunity
Follicular helper T cells promote antibody production by B cells, and regulatory B cells, in turn, can restrain T cell activation. Here, Khan et al. show that PD-L1 plays a critical role in regulatory B cell function, curbing excessive immune responses by engaging the PD-1 receptor on follicular helper T cells.
- Adnan R. Khan
- , Emily Hams
- & Padraic G. Fallon
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Article
| Open AccessStructure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase
Lytic polysaccharide monooxygenases (LPMOs) are industrially important enzymes that oxidatively deconstruct polysaccharides. Here, Lo Leggio et al. report the activity, spectroscopy and three-dimensional structure of a LPMO of the new CAZy AA13 family active on recalcitrant-retrograded starch.
- Leila Lo Leggio
- , Thomas J. Simmons
- & Paul H. Walton
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An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
Standard ChIP-seq protocols require large numbers of cells for high-quality datasets, limiting the application of this technique on rare cell types. Here, Brind’Amour et al. introduce an ultra-low-input ChIP-seq protocol to generate maps of covalent histone marks from as few as 1,000 cells.
- Julie Brind’Amour
- , Sheng Liu
- & Matthew C. Lorincz
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Sequencing of first-strand cDNA library reveals full-length transcriptomes
Strand-specific RNA-seq (ssRNA-seq) data often lack information on 5′ and 3′ ends of transcripts. Here the authors present a novel method for ssRNA-seq that enables the simultaneous profiling of gene expression, TSSs and polyadenylation sites at near-base resolution with a single library.
- Saurabh Agarwal
- , Todd S. Macfarlan
- & Shigeki Iwase
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Profiling lymphocyte interactions at the single-cell level by microfluidic cell pairing
Direct cell–cell interactions form the basis of the adaptive immune response. Here, Dura et al.present an advanced microfluidic platform that enables highly parallel pairing of primary immune cells and multiparametric and dynamic measurements of lymphocyte interactions and activation processes.
- Burak Dura
- , Stephanie K. Dougan
- & Joel Voldman
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Article
| Open AccessHigh-quality genome (re)assembly using chromosomal contact data
The correct assembly of genomes from sequencing data remains a challenge due to difficulties in correctly assigning the location of repeated DNA elements. Here the authors describe GRAAL, an algorithm that utilizes genome-wide chromosome contact data within a probabilistic framework to produce accurate genome assemblies.
- Hervé Marie-Nelly
- , Martial Marbouty
- & Romain Koszul
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An artificial PPR scaffold for programmable RNA recognition
Pentatricopeptide repeat (PPR) proteins bind RNA and control diverse aspects of RNA metabolism in eukaryotic cells. Here, Coquille et al.present the crystal structures of several engineered PPR domains, elucidate their RNA binding mode and suggest paths to the design of modular, sequence-specific PPR domains.
- Sandrine Coquille
- , Aleksandra Filipovska
- & Oliver Rackham
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| Open AccessCell type-specific delivery of short interfering RNAs by dye-functionalised theranostic nanoparticles
A potential drug should specifically interact with its intended target in order to limit unwanted side effects. Here, the authors fabricate a biodegradable polymer nanoparticle with a fluorescent hepatic uptake transporter ligand to achieve targeted in vivosiRNA delivery and imaging of delivery.
- Adrian T. Press
- , Anja Traeger
- & Michael Bauer
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Somatic transcriptome priming gates lineage-specific differentiation potential of human-induced pluripotent stem cell states
Molecular and functional differences between induced pluripotent stem cells (iPSCs) derived from distinct cell types have been described. Here the authors show, by comparing human iPSCs derived from fibroblasts or cord blood, that the competence in activating developmental genes upon differentiation is influenced by the donor cell of origin.
- Jong-Hee Lee
- , Jung Bok Lee
- & Mickie Bhatia
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TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis
Genome editing has yet to be performed in non-bilaterian phyla. Here, Ikmi et al. develop techniques to use both TALEN and CRISPR/Cas9 in the sea anemone, Nematostella vectensis, and further leverage a locus expressing an endogenous fluorescent protein as a landing site for homologous recombination-mediated transgenesis.
- Aissam Ikmi
- , Sean A. McKinney
- & Matthew C. Gibson
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Semi-permeable coatings fabricated from comb-polymers efficiently protect proteins in vivo
The attachment of polymers to protein molecules is known to shield them from biological breakdown. Here, the authors apply this concept to an asparaginase, in order to prevent its deactiviation by host immune responses during leukaemia treatment.
- Mi Liu
- , Pål Johansen
- & Marc A. Gauthier
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Article
| Open AccessMind-controlled transgene expression by a wireless-powered optogenetic designer cell implant
Brain–machine interfaces offer the possibility of controlling prosthetic devices using changes in brain activity. Folcher et al.couple such a system wirelessly to an optogenetic implant in mice to control expression of a transgene, demonstrating its potential for mind-controlled drug delivery.
- Marc Folcher
- , Sabine Oesterle
- & Martin Fussenegger
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Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells
Tools derived from synthetic biology offer powerful means to refine drug delivery and disease detection. Liu et al. engineer a logical AND gate using CRISPR-Cas9 to drive gene expression only cells in which two promoters are active, and use it to selectively inhibit the growth of bladder cancer cells in vitro.
- Yuchen Liu
- , Yayue Zeng
- & Zhiming Cai
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CD95 and CD95L promote and protect cancer stem cells
The death receptor CD95/Fas induces apoptosis of many normal cells but prevents necrotic death of cancer cells. Here the authors demonstrate that CD95 activation promotes a cancer stem cell (CSC) phenotype, and that CSCs but not differentiated cancer cells are resistant to CD95-mediated apoptosis and depend on CD95 signalling to prevent necrosis.
- Paolo Ceppi
- , Abbas Hadji
- & Marcus E. Peter
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MS-GF+ makes progress towards a universal database search tool for proteomics
The development of software tools to analyse large mass spectrometry data sets lags behind the increase in diversity of the data. Here the authors develop MS-GF+, a database search tool that outperforms other popular tools in identifying peptides from a variety of data sets.
- Sangtae Kim
- & Pavel A. Pevzner
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A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations
Phage-assisted continuous evolution (PACE) has the potential to rapidly evolve drug-resistant mutations. Here, Dickinson et al.present a protease PACE system that identifies clinically relevant mutations conferring resistance to protease inhibitors in only a few days of continuous evolution.
- Bryan C. Dickinson
- , Michael S. Packer
- & David R. Liu
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Article
| Open AccessVesicle-based artificial cells as chemical microreactors with spatially segregated reaction pathways
In biological systems, cells are divided into compartments, typically with lipid layers. Here, the authors design a multipart vesicle system for sequential enzymatic reactions, where the product from one reaction traverses into the next, allowing multiple spatially separated reaction steps.
- Yuval Elani
- , Robert V. Law
- & Oscar Ces
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An authentic imaging probe to track cell fate from beginning to end
The availability of tracers to track the health of cells over long periods of time will be of value to optimize cell-based therapy. Here, Lee et al.design a nanoparticle that fluoresces red in living cells, but fluoresces green when cells begin to die from apoptosis or necrosis.
- Seung Koo Lee
- , Luke J. Mortensen
- & Ching-Hsuan Tung
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Highly modular bow-tie gene circuits with programmable dynamic behaviour
Engineering gene expression systems that can be programmed to respond to specific environmental conditions is challenging. Here, the authors develop a synthetic bow-tie circuit that is able to sense signals from microRNA molecules and affect a change in protein dynamics in mammalian cells.
- Laura Prochazka
- , Bartolomeo Angelici
- & Yaakov Benenson
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Magneto-fluorescent core-shell supernanoparticles
Magneto-fluorescent nanoparticles hold promise for bioimaging applications, but synthesizing uniform particles with tunable sizes remains challenging. Chen et al. propose an approach for co-assembling magnetic particles with fluorescent quantum dots, leading to well-defined core-shell structures.
- Ou Chen
- , Lars Riedemann
- & Moungi G. Bawendi
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Article
| Open AccessCombining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice
Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.
- Wanneng Yang
- , Zilong Guo
- & Lizhong Xiong
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Enzyme activity in liquid lipase melts as a step towards solvent-free biology at 150 °C
Enzymatic reactions typically occur in aqueous media or with hydrated enzymes. Here, the authors form fluid enzyme-polymer conjugates with sub-solvation levels of water, and demonstrate catalytic hydrolysis in the absence of a solvent at high temperatures.
- Alex P. S. Brogan
- , Kamendra P. Sharma
- & Stephen Mann
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Continuous wireless pressure monitoring and mapping with ultra-small passive sensors for health monitoring and critical care
Continuous monitoring of physiological parameters in clinical practice requires wired connections to the sensors that are attached to or implanted in patients. Here, Chen et al. demonstrate a wireless, millimetre-scale sensor, which can monitor intracranial pressure of mice in real-time.
- Lisa Y. Chen
- , Benjamin C. -K. Tee
- & Zhenan Bao
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A bistable genetic switch based on designable DNA-binding domains
Toggle switches can be engineered using pairs of transcriptional repressors; however, their bistability depends on nonlinear DNA-binding properties. Lebar et al. design a circuit that ensures bistability by artificially generating nonlinearity and use it to construct a toggle from programmable DNA-binding domains.
- Tina Lebar
- , Urban Bezeljak
- & Roman Jerala
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Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol
Microbial pathways can be engineered for the sustainable production of chemical products such as transportation fuels. Here the authors design and implement a de novo biosynthetic pathway in E. colithat is capable of producing the gasoline replacement, 4-methyl-pentanol.
- Micah J. Sheppard
- , Aditya M. Kunjapur
- & Kristala L. J. Prather
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Programmable biofilm-based materials from engineered curli nanofibres
Bacterial cells use a self-generated extracellular matrix of various biomolecules in order to form biofilms and promote their stability. Here, the authors present a method for genetically controlling the composition of this extracellular matrix to yield more functional biofilms.
- Peter Q. Nguyen
- , Zsofia Botyanszki
- & Neel S. Joshi
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Article
| Open AccessMagnetic antibody-linked nanomatchmakers for therapeutic cell targeting
Cell therapy requires sufficient amounts of therapeutic cells to be delivered to the injured tissue. Here the authors use magnetic iron nanoparticles conjugated with antibodies that bind therapeutic cells and cardiomyocytes to treat myocardial ischemia/reperfusion injury in rats and show that targeting to the heart is enhanced upon local application of a magnetic field.
- Ke Cheng
- , Deliang Shen
- & Eduardo Marbán
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Article
| Open AccessProtein co-translocational unfolding depends on the direction of pulling
Protein unfolding and translocation through membrane pores occurs in several biological processes and has implications in nanopore technologies. Here, the authors show that the kinetics of unfolding differ depending on which end of the chain enters the pore first.
- David Rodriguez-Larrea
- & Hagan Bayley
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Microfluidic platform for the quantitative analysis of leukocyte migration signatures
Current leukocyte migration assays usually report bulk attractive behaviour of cells within a chemokine gradient. Here, the authors develop a microfluidic device to simultaneously measure several migration responses on exposure to commonly used leukocyte chemokines, and report previously unrecognized cell behaviour.
- Leo Boneschansker
- , Jun Yan
- & Daniel Irimia
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Article
| Open AccessAn engineered pathway for the biosynthesis of renewable propane
Propane is the main component of liquid petroleum gas and has a wide variety of commercial applications. Here, the authors engineer a synthetic metabolic pathway in E. coli, and demonstrate for the first time the renewable production of propane.
- Pauli Kallio
- , András Pásztor
- & Patrik R. Jones
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Article
| Open AccessA genome-wide map of hyper-edited RNA reveals numerous new sites
Common methods to detect adenosine-to-inosine RNA editing sites rely on mapping short RNA reads to the genome while allowing only a limited number of mismatches. Here, Porath et al. present a novel RNA-seq based approach to identify hyper-edited reads that significantly expands the RNA editome.
- Hagit T. Porath
- , Shai Carmi
- & Erez Y. Levanon
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A smart and versatile theranostic nanomedicine platform based on nanoporphyrin
Nanoparticles can be used for therapeutic and diagnostic purposes. Here, the authors report that nanoparticles made of a single chemical building block, called nanoporphyrins, incorporate eight different functionalities, including various types of imaging, drug delivery and cancer therapy.
- Yuanpei Li
- , Tzu-yin Lin
- & Kit S. Lam
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Enhancement of biological reactions on cell surfaces via macromolecular crowding
Optimizing cell-surface biological reactions is an important goal of biotechnology and industrial processes. Here the authors use macromolecular crowding to enhance the enzymatic conversion of red blood cells to the universal type O blood type, using orders of magnitude less enzyme than was previously required.
- Rafi Chapanian
- , David H. Kwan
- & Jayachandran N Kizhakkedathu
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Expansion of the CRISPR–Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs
Current CRISPR-mediated genome-editing methods are limited by the requirement for a specific +1 nucleotide when using the U6 promoter to drive guide RNA synthesis. Now, Ranganathan et al.report a modification of the CRISPR–Cas9 system that more than doubles the number of targetable CRISPR sites within the human genome.
- Vinod Ranganathan
- , Karl Wahlin
- & Donald J. Zack
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Conformable amplified lead zirconate titanate sensors with enhanced piezoelectric response for cutaneous pressure monitoring
The development of more sensitive tools for physiological monitoring presents obvious advantages in health-care and diagnostic assessment. Here, the authors present a thin, skin-like sensor that uses enhanced responses in lead zirconate titanate for monitoring arterial pressure waves.
- Canan Dagdeviren
- , Yewang Su
- & John A. Rogers
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Metabolic engineering of Corynebacterium glutamicum for L-arginine production
The amino acid, L-arginine, has important applications in the food, pharmaceutical and cosmetics industries. Here the authors systematically engineer a Corynebacterium glutamicum strain for the production of L-arginine, and show that their metabolic engineering approach can be used for the industrial production of valuable chemicals.
- Seok Hyun Park
- , Hyun Uk Kim
- & Sang Yup Lee
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Article
| Open AccessA designer cell-based histamine-specific human allergy profiler
The advancement of sensitive, accurate and non-invasive methods to identify the allergen that drives allergic disease in an individual remains a challenge. Here, the authors develop a synthetic biology approach using human designer cells to profile allergic reactions against an array of allergens measuring histamine release from whole blood.
- David Ausländer
- , Benjamin Eggerschwiler
- & Martin Fussenegger
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Modulating the frequency and bias of stochastic switching to control phenotypic variation
Mechanisms that control gene expression variation in cells can affect factors such as population growth and adaptability. Here, the authors present a strategy that allows both the level and amount of variation in gene expression to be tuned in E. coli populations using the fimswitch.
- Michelle Hung
- , Emily Chang
- & Han N. Lim
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Article
| Open AccessCreation of a gated antibody as a conditionally functional synthetic protein
The ability to control antibody binding could have important medical implications. Here, the authors present a method to engineer phosphatase-controllable antibodies that bind to a specific recognition site in the presence of two biomarker inputs.
- Smita B. Gunnoo
- , Helene M. Finney
- & Benjamin G. Davis
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Poking cells for efficient vector-free intracellular delivery
The incorporation of foreign objects into cells can be used in various avenues of biological research, although crossing the cell membrane can be challenging. Here, the authors use a diamond nanoneedle array for enhanced delivery of various particles into cells, including neurons.
- Ying Wang
- , Yang Yang
- & Peng Shi
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Article
| Open AccessEngineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells
Designing inducible and reversible nuclear localization signals would enable researchers to dissect and engineer cellular networks. Here Niopek et al.create a light-inducible nuclear localization signal to regulate gene expression and mitosis in mammalian cells, using blue light.
- Dominik Niopek
- , Dirk Benzinger
- & Barbara Di Ventura
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Synergistic roles for lipids and proteins in the permanent adhesive of barnacle larvae
Using their unique bioadhesives, barnacles can adhere to a great variety of surfaces. Here, Gohad et al.show that the barnacle larval bioadhesive contains lipids and phosphoproteins that are organized in a complex structure and work together to maximize adhesion.
- Neeraj V. Gohad
- , Nick Aldred
- & Andrew S. Mount
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IgGs are made for walking on bacterial and viral surfaces
Antibody–antigen recognition is one of the important aspects of immunity, but the nanomechanical process of this recognition is not fully understood. Here, using high-speed atomic force microscopy, the authors observe that on membranes containing a high density of immobile antigens antibodies move in a ‘random walking’ motion.
- Johannes Preiner
- , Noriyuki Kodera
- & Peter Hinterdorfer
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