Biotechnology

  • Article
    | Open Access

    Worldwide pandemics of obesity and diabetes prompt an urgent need for new approaches to their prevention and cure. Here the authors present a CRISPR-based strategy that enhances the therapeutic potential of human adipocytes when implanted in obese mice.

    • Emmanouela Tsagkaraki
    • , Sarah M. Nicoloro
    •  & Michael P. Czech
  • Article
    | Open Access

    Bone implants with antibacterial and osteogenic properties are important for clinical applications, but creating both properties simultaneously remains challenging. Here, the authors demonstrate a self-activating implant using a hydroxyapatite and molybdenum disulfide coating which accelerates bone regeneration and at the same time prevents bacterial infection.

    • Jieni Fu
    • , Weidong Zhu
    •  & Shuilin Wu
  • Article
    | Open Access

    Engineering biosynthetic assembly lines is a powerful path to new natural products but is challenging with current methods. Here the authors use CRISPR-Cas9 to exchange subdomains within NRPS to alter substrate selectivity.

    • Wei Li Thong
    • , Yingxin Zhang
    •  & Jason Micklefield
  • Article
    | Open Access

    Microbial ecosystem-based bioproduction requires the regulation of phenotypic structure of microbial populations. Here, the authors report the construction of a programmed lysis system and its ability for reprograming microbial cooperation in poly(lactate-co-3-hydroxybutyrate) and butyrate production by E. coli strains.

    • Wenwen Diao
    • , Liang Guo
    •  & Liming Liu
  • Article
    | Open Access

    Rational design of enzymes with new or improved properties is rarely straightforward, and artificial selection pressure approaches that link an improvement in the target to cell growth are an alternative. Here, the authors show that diverse enzymes sharing the ubiquitous cofactor NAD(P)+ can substitute for defective NAD+ regeneration, representing a very broadly-applicable artificial selection.

    • Lara Sellés Vidal
    • , James W. Murray
    •  & John T. Heap
  • Article
    | Open Access

    The testing of engineered enzymes represents a bottleneck. Here the authors report a screening method combining microfluidics and mass spectrometry, to map the catalysis of a mutated enzyme, characterise the range of products generated and recover the sequences of variants with desired activities.

    • Linfeng Xu
    • , Kai-Chun Chang
    •  & Adam R. Abate
  • Article
    | Open Access

    The extracellular matrix contributes to tissue regeneration by binding and releasing growth factors. Here the authors present the jigsaw-shaped self-assembling peptide JigSAP as an artificial ECM and show that VEGF-JigSAP has therapeutic effects on the subacute-chronic phase of brain stroke.

    • Atsuya Yaguchi
    • , Mio Oshikawa
    •  & Itsuki Ajioka
  • Article
    | Open Access

    Organizing centers act to pattern surrounding tissues during embryogenesis through the secretion of morphogens. Here the authors model human organizers using light stimulus to geometrically confine SHH expression in differentiating hESCs, generating spatially resolved proximal distal patterns.

    • Riccardo De Santis
    • , Fred Etoc
    •  & Ali H. Brivanlou
  • Article
    | Open Access

    GAPDH is generally considered a housekeeping gene and functions in glycolysis. Here, the authors show that GAPDH has a role in promoting vesicle clustering in endosomes and can load siRNA onto the surface of extracellular vesicles, which can be exploited therapeutically.

    • Ghulam Hassan Dar
    • , Cláudia C. Mendes
    •  & Matthew J. A. Wood
  • Article
    | Open Access

    Certain bovine antibodies have ultra-long long complementarity-determining regions (CDRs) that contain a knob for antigen interaction, which is connected to the antibody through a stalk. Here, the authors combine biophysical experiments and MD simulations and show that the stalk length is critical for the folding and stability of these antibodies. The authors also demonstrate that ultra-long bovine CDRs can be grafted into human antibodies, and furthermore show that de novo designed mini-domains that bind to the SARS-CoV-2 spike protein with high affinity can be integrated as a knob in ultra-long CDRs in bovine and human antibodies, which neutralize SARS-CoV-2.

    • Hristo L. Svilenov
    • , Julia Sacherl
    •  & Johannes Buchner
  • Article
    | Open Access

    Traditional synthetic biology tools operate by complex re-programming of DNA, requiring significant amount of ‘nucleotide-based code’ to implement instructions that are transcribed at the protein level. Here the authors demonstrate the direct regulation of cellular phenotype at the single-protein level by creating a two-input logic gate for biological computation using ‘allosteric wiring’.

    • Yashavantha L. Vishweshwaraiah
    • , Jiaxing Chen
    •  & Nikolay V. Dokholyan
  • Article
    | Open Access

    Insect-like biomimetic compound eyes have many technological applications. Here, the authors present a facile fabrication scheme involving microfluidics assisted 3D printing that permits to completely separate design, optimization and construction of optical and sensor components.

    • Bo Dai
    • , Liang Zhang
    •  & Dawei Zhang
  • Article
    | Open Access

    Morphogens disperse to pattern tissues and control their growth during development, allowing for the specification of multiple fates across space. Here the authors block dispersal of a morphogen Dpp (BMP2/4) and show that the requirement for Dpp dispersal is much lower than previously thought.

    • Shinya Matsuda
    • , Jonas V. Schaefer
    •  & Markus Affolter
  • Article
    | Open Access

    The exact protein features that control passage through the eukaryotic secretory system remain largely unknown. Here the authors report SECRiFY which they use to evaluate the secretory potential of polypeptides on a proteome-wide scale in yeast, revealing a role for flexibility and intrinsic disorder.

    • Morgane Boone
    • , Pathmanaban Ramasamy
    •  & Nico Callewaert
  • Article
    | Open Access

    Heterotopic ossification (HO) is the formation of pathological mature bone within extraskeletal soft tissues, and there are currently no reliable methods for removing these calcified plaques. Here, the authors demonstrate that chemically engineered osteoclasts coated with tetracycline can improve their targeting capacity to ectopic calcifications, which extends their bone resorption functions for the treatment of HO.

    • Wenjing Jin
    • , Xianfeng Lin
    •  & Ruikang Tang
  • Article
    | Open Access

    Peptide secondary metabolites have a diverse range of functions. Here the authors present a method to design and screen a large library of modified peptides in E. coli against a target of interest.

    • Andrew M. King
    • , Daniel A. Anderson
    •  & Christopher A. Voigt
  • Article
    | Open Access

    Aptamers could potentially be widely used in therapy and diagnostics. Here the authors use standardised assay conditions to compare aptamer properties in tumour targeting.

    • Linsley Kelly
    • , Keith E. Maier
    •  & Matthew Levy
  • Article
    | Open Access

    The role of the post-translational modifications in tissue regeneration is still not clearly understood. Here, the authors show that many nuclear proteins change S-nitrosylation state in the regenerating zebrafish tailfin, highlighting the importance of Kdm1a S-nitrosylation in the repair process.

    • Gianfranco Matrone
    • , Sung Yun Jung
    •  & John P. Cooke
  • Article
    | Open Access

    Long-term expression of Cas9 following precision genome editing in vivo may lead to undesirable consequences. Here we show that a single-vector, self-inactivating AAV system containing Cas9 nuclease, guide, and DNA donor can use homology-directed repair to correct disease mutations in vivo.

    • Raed Ibraheim
    • , Phillip W. L. Tai
    •  & Erik J. Sontheimer
  • Article
    | Open Access

    Single-cell proteomics is an emerging technology but protein coverage, throughput and quantitation accuracy are often still insufficient. Here, the authors develop a nested nanowell chip that improves protein recovery, throughput and robustness of isobaric labeling-based quantitative single-cell proteomics.

    • Jongmin Woo
    • , Sarah M. Williams
    •  & Ying Zhu
  • Article
    | Open Access

    Mesenchymal stem cells adopt differentiation pathways based upon mechanical cues in their environment which change throughout development. Here the authors develop a material and culture system to modify and measure the degree to which cells retain cumulative effects of mechanosensing to explore how cells erase the memory of some cues while locking in memory of others.

    • Cheng Zhang
    • , Hongyuan Zhu
    •  & Min Lin
  • Article
    | Open Access

    Vascularization is critical for cranial bone growth, maintenance, and healing, but it remains unknown how blood vessels are spatially distributed in the calvarium, and how they interact with skeletal progenitors during these processes. Here, the authors apply a quantitative light-sheet imaging platform to visualize and analyze the relationship between blood vessels and skeletal progenitors throughout the murine calvarium.

    • Alexandra N. Rindone
    • , Xiaonan Liu
    •  & Warren L. Grayson
  • Article
    | Open Access

    Returning from Mars to Earth requires propellant. The authors propose a biotechnology-enabled in situ resource utilization (bioISRU) process to produce a Mars specific rocket propellant, 2,3-butanediol, using cyanobacteria and engineered E. coli, with lower payload mass and energy usage compared to chemical ISRU strategies.

    • Nicholas S. Kruyer
    • , Matthew J. Realff
    •  & Pamela Peralta-Yahya
  • Article
    | Open Access

    The independent control of substrate stiffness and tethering of extracellular matrix to substrates for mechanical signalling investigations remains challenging. Here the authors present StemBond hydrogels, with stable ECM tethering that can be varied independently of stiffness, and use these to modulate the function of mouse and human pluripotent stem cells.

    • Céline Labouesse
    • , Bao Xiu Tan
    •  & Kevin J. Chalut
  • Article
    | Open Access

    Quantification of rare somatic mutations is essential for basic research and translational applications. Here the authors present Quantitative Blocker Displacement Amplification allowing for accurate detection of mutations below 0.01% VAF.

    • Peng Dai
    • , Lucia Ruojia Wu
    •  & David Yu Zhang
  • Article
    | Open Access

    The limited ability of cancer therapeutics in crossing the cancer cell membrane hampers their therapeutic potential. Here, the authors report Salmonella-based system for intracellular delivery of protein drugs, e.g. caspase-3, and show reduction of tumors in mouse models of breast and liver cancer.

    • Vishnu Raman
    • , Nele Van Dessel
    •  & Neil S. Forbes
  • Article
    | Open Access

    Isoflavonoids are a class of industrially important plant natural products, but their low abundance and structural complexity limits their availability. Here, the authors engineer Saccharomyces cerevisiae metabolism to become a platform for efficient production of daidzein which is core chemical scaffold for isoflavonoid biosynthesis, and show its application for production of bioactive glucosides from glucose.

    • Quanli Liu
    • , Yi Liu
    •  & Jens Nielsen
  • Article
    | Open Access

    Heterologous expression of recombinant proteins often results in misfolding, aggregation and degradation. Here, we show an in vivo dual-biosensor system that simultaneously assesses protein translation and protein folding, thereby enabling rapid screening of expression strains as well as mutant libraries.

    • Ariane Zutz
    • , Louise Hamborg
    •  & Alex Toftgaard Nielsen
  • Article
    | Open Access

    RNA-protein interactions play critical roles in post-transcriptional gene regulation. Here the authors demonstrate pRBS-ID, an updated MS/MS-based method that combines the benefits of photoactivatable ribonucleosides and the chemical cleavage of RNA.

    • Jong Woo Bae
    • , Sangtae Kim
    •  & Jong-Seo Kim
  • Article
    | Open Access

    The directed evolution of antibodies yields important tools for research and therapy. Here the authors develop a periplasmic phage-assisted continuous evolution platform for improvement of protein-protein interactions in the disulfidecompatible E. coli periplasm.

    • Mary S. Morrison
    • , Tina Wang
    •  & David R. Liu
  • Article
    | Open Access

    Leptomeningeal disease (LMD) is a serious complication of metastatic solid tumors with a poor prognosis. Here, by using single-cell RNA sequencing of cerebrospinal fluid, the authors report genomic and immune correlates of response to immunotherapy in two cohorts of patients with LMD treated with immune checkpoint inhibitors.

    • Sanjay M. Prakadan
    • , Christopher A. Alvarez-Breckenridge
    •  & Alex K. Shalek
  • Article
    | Open Access

    Genome engineering is challenging compared to plasmid DNA manipulation. Here the authors create a simple methodology called SEGA that enables genome engineering by combining DNA and bacterial cells followed by identification of recombinant clones by a change in colour when grown on agar plates.

    • Carolyn N. Bayer
    • , Maja Rennig
    •  & Morten H. H. Nørholm
  • Perspective
    | Open Access

    The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.

    • Chengxin Dai
    • , Anja Füllgrabe
    •  & Yasset Perez-Riverol
  • Article
    | Open Access

    Cell encapsulation into biomaterials for transplantation is currently limited by inadequate oxygenation. Here the authors present a biomimetic scaffold featuring internal continuous air channels endowed with 10,000-fold higher O2 diffusivity than hydrogels and demonstrate correction of diabetes in immunocompetent mice using rat islets for over 6 months.

    • Long-Hai Wang
    • , Alexander Ulrich Ernst
    •  & Minglin Ma
  • Article
    | Open Access

    The prediction of major cardiovascular events is still an unsolved problem. Here, the authors present a multi-color, multi-targeted non-invasive imaging technology that allows reliable in vivo identification of silent but prognostically highly relevant danger patterns prior to myocardial infarction in mice.

    • Ulrich Flögel
    • , Sebastian Temme
    •  & Bodo Levkau
  • Article
    | Open Access

    Fatty acyl reductases (FARs) are critical enzymes in the biosynthesis of fatty alcohols and have the ability to directly acces acyl-ACP substrates. Here, authors couple machine learning-based protein engineering framework with gene shuffling to optimize a FAR for the activity on acyl-ACP and improve fatty alcohol production.

    • Jonathan C. Greenhalgh
    • , Sarah A. Fahlberg
    •  & Philip A. Romero
  • Article
    | Open Access

    Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.

    • Florian Leonardus Rudolfus Lucas
    • , Roderick Corstiaan Abraham Versloot
    •  & Giovanni Maglia
  • Article
    | Open Access

    Simultaneous detection of multiple analytes from a sample is currently difficult. Here the authors present protocell arrays in a customisable platform integrating cell-free expression with a polymer-based aqueous two-phase system; they use this for detection of chemically diverse targets from biofluids.

    • Yan Zhang
    • , Taisuke Kojima
    •  & Mark P. Styczynski
  • Article
    | Open Access

    In vitro protein folding can often result in aggregation and low yields. Here the authors use nanoscale exoshells to improve soluble yield, functional yield and specific activity of folded proteins.

    • Samira Sadeghi
    • , Siddharth Deshpande
    •  & Chester L. Drum
  • Article
    | Open Access

    Genetic code expansion strategies are limited to specific codons that can be reassigned to new amino acids. Here the authors show that quadruplet-decoding tRNAs (qtRNAs) can be rapidly discovered and evolved to decode new quadruplet codons, enabling four independent decoding events in a single protein in living cells.

    • Erika A. DeBenedictis
    • , Gavriela D. Carver
    •  & Ahmed H. Badran
  • Article
    | Open Access

    Differential expression analysis of single-cell transcriptomics allows scientists to dissect cell-type-specific responses to biological perturbations. Here, the authors show that many commonly used methods are biased and can produce false discoveries.

    • Jordan W. Squair
    • , Matthieu Gautier
    •  & Grégoire Courtine