Biotechnology articles within Nature Communications

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  • Review Article
    | Open Access

    Our efforts to build complex synthetic biology circuits are impeded by limited knowledge of optimal combinations. In this review, the authors consider current combinatorial methods and look to emerging technologies.

    • Gita Naseri
    •  & Mattheos A. G. Koffas

  • Article
    | Open Access

    TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.

    • Nan Jiang
    • , Aimer Gutierrez-Diaz
    •  & Erich Grotewold

  • Article
    | Open Access

    The spatial organisation of microbial communities is caused by the interplay of biotic and abiotic factors. Here the authors design a microfluidic platform to quantify the spatiotemporal parameters influencing diffusion-mediated interactions, and use this device to investigate information transmission and metabolic cross-feeding in synthetic microbial consortia.

    • Sonali Gupta
    • , Tyler D. Ross
    •  & Ophelia S. Venturelli

  • Article
    | Open Access

    The type III secretion system (T3SS) of bacteria can be used to inject cargo into eukaryotic cells but its lack of target specificity is a disadvantage. Here the authors place the T3SS under the regulation of light by engineering optogenetic switches into the dynamic cytosolic T3SS component SctQ.

    • Florian Lindner
    • , Bailey Milne-Davies
    •  & Andreas Diepold

  • Article
    | Open Access

    Noninvasive detection of molecular targets in living subjects could provide valuable insights into healthy function and disease. Here, the authors develop vasoactive imaging probes which allow wide-field in vivo mapping of nanomolar-level molecular species in rat brain.

    • Robert Ohlendorf
    • , Agata Wiśniowska
    •  & Alan Jasanoff

  • Article
    | Open Access

    Most human protein-coding genes are expressed as multiple isoforms. Here the authors present ORF Capture-seq that uses cloned ORFs as probes to capture and sequence full length transcript sequences. This enables highly sensitive characterization of eukaryotic transcriptomes.

    • Gloria M. Sheynkman
    • , Katharine S. Tuttle
    •  & Marc Vidal

  • Article
    | Open Access

    Exosomes are used as disease biomarkers, but their characterization in biological samples is challenging. Here the authors achieve simultaneous characterization of size and zeta potential of individual nanoparticles and particle mixtures at physiological salinity conditions, exploiting a salt gradient in a capillary channel.

    • Martin K. Rasmussen
    • , Jonas N. Pedersen
    •  & Rodolphe Marie

  • Article
    | Open Access

    Manipulation of genes controlling microbial shapes can affect bio-production. Here, the authors employ an optogenetic method to realize dynamic morphological engineering of E. coli replication and division and show the increased production of acetoin and poly(lactate-co-3-hydroxybutyrate).

    • Qiang Ding
    • , Danlei Ma
    •  & Xiulai Chen

  • Article
    | Open Access

    Lactazole A is a thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, the authors show a platform for in vitro biosynthesis of lactazole A via a combination of a flexible in vitro translation system with recombinantly produced lactazole biosynthetic enzymes.

    • Alexander A. Vinogradov
    • , Morito Shimomura
    •  & Hiroyasu Onaka

  • Article
    | Open Access

    Biofilm formation is a major problem in indwelling medical devices. Here, the authors report on the development of a magnetically responsive micro pillar surface for the controlled prevention and removal of biofilms which also increased sensitivity to antibiotics.

    • Huan Gu
    • , Sang Won Lee
    •  & Dacheng Ren

  • Article
    | Open Access

    Arterial degeneration, closely associated with cardiovascular diseases, is driven by aging-related vascular cell-specific transcriptomics changes. This study provides a single-cell transcriptomic atlas for senile aortic and coronary arteries and underscores FOXO3A-based the transcriptional network in vasoprotection during aging.

    • Weiqi Zhang
    • , Shu Zhang
    •  & Jing Qu

  • Article
    | Open Access

    Previous versions of photoactivatable Cre recombinase (PA-Cre) suffered from unintentional recombination in dark conditions. Here, the authors develop an improved version of PA-Cre, called PA-Cre 3.0, which shows reduced leakiness and improved efficiency upon activation, and make mouse lines that express PA-Cre 3.0 conditionally.

    • Kumi Morikawa
    • , Kazuhiro Furuhashi
    •  & Masayuki Yazawa

  • Article
    | Open Access

    Fermentation parameters of industrial processes are often not the ideal growth conditions for industrial microbes. Here, the authors reveal that young genes are more responsive to environmental stress than ancient genes using a new gene age assignment method and provide targeted genes for metabolic engineering.

    • Tyler W. Doughty
    • , Iván Domenzain
    •  & John P. Morrissey

  • Article
    | Open Access

    Precise patterning of lipid-stabilised aqueous droplets is a key challenge in building synthetic tissue designs. Here, the authors show how the interactions between pairs of droplets direct the packing of droplets within 3D-printed networks, enabling the formation of synthetic tissues with high-resolution features.

    • Alessandro Alcinesio
    • , Oliver J. Meacock
    •  & Hagan Bayley

  • Article
    | Open Access

    A small set of promoters is used for most genetic construct design in S. cerevisiae. Here, the authors develop a predictive model of promoter activity trained on a data set of over one million sequences and use it to design large sets of high-activity promoters.

    • Benjamin J. Kotopka
    •  & Christina D. Smolke

  • Article
    | Open Access

    Sorting insects based on sex is error prone and frequently labour intensive. Here, the authors present a drug-inducible sex separation system based on sex-specific rescue from antibotic toxicity.

    • Nikolay P. Kandul
    • , Junru Liu
    •  & Omar S. Akbari

  • Article
    | Open Access

    Many industrial organisms are the result of recent or ancient allopolypoidy events. Here the authors iteratively combine the genomes of six yeast species to generate a viable hybrid.

    • David Peris
    • , William G. Alexander
    •  & Chris Todd Hittinger

  • Article
    | Open Access

    Targeted delivery of nanomaterials to subcellular compartments could allow precision engineering of plant function. Here, Santana et al. show that quantum dots functionalized with a rationally-designed targeting peptide are preferentially delivered to chloroplasts where they can be used to tune organellar redox status.

    • Israel Santana
    • , Honghong Wu
    •  & Juan Pablo Giraldo

  • Article
    | Open Access

    Malate dehydrogenase (MDH) is one of the key enzymes for succinic acid (SA) bioproduction. Here, the authors report biochemical and structural analyses of various MDHs to reveal amino acids influencing the specific activity and susceptibility to substrate inhibition, and achieve industrial-level SA production.

    • Jung Ho Ahn
    • , Hogyun Seo
    •  & Sang Yup Lee

  • Article
    | Open Access

    Corn fiber is a difficult feedstock to utilize due to its recalcitrant hemicellulose. Here, the authors characterize the recalcitrant structures, isolate a new bacterium to consume the hemicellulose, identify its enzymes, and show the benefit with increased conversion of corn fiber to ethanol.

    • Dhananjay Beri
    • , William S. York
    •  & Christopher D. Herring

  • Article
    | Open Access

    Ribosome engineering is an emerging powerful approach for synthetic protein synthesis. Here the authors invert the Ribo-T system, using the engineered ribosome to translate the proteome while the native ribosome translates specific mRNA.

    • Nikolay A. Aleksashin
    • , Teresa Szal
    •  & Alexander S. Mankin

  • Article
    | Open Access

    Therapeutic siRNA becomes trapped in endosomes, limiting its efficacy. Here the authors use fluorescently-tagged galectin-9 as a biosensor for membrane damage to monitor endosomal escape of cholesterol-conjugated siRNA following treatment of small molecule membrane-destabilising drugs.

    • Hampus Du Rietz
    • , Hampus Hedlund
    •  & Anders Wittrup

  • Article
    | Open Access

    Combining genome mining and heterologous expression in a genetically tractable host can lead to bioactive natural products discovery and production. Here, the authors employ this strategy for new decalin-containing diterpenoid pyrenes production by expressing native, extended, and shunt pathways in Aspergillus oryzae.

    • Kento Tsukada
    • , Shono Shinki
    •  & Teigo Asai

  • Article
    | Open Access

    Protein aggregation remains a significant challenge for manufacturing of protein biopharmaceuticals. Here, the authors demonstrate the use of directed evolution and an assay for in vivo innate protein aggregation-propensity to generate aggregation-resistant scFv fragments.

    • Jessica S. Ebo
    • , Janet C. Saunders
    •  & David J. Brockwell

  • Article
    | Open Access

    Current synthetic DNA-based data storage systems have high recording costs, read-write latency and error-rates that make them uncompetitive compared to traditional digital storage. The authors use nicks in native DNA to encode data in parallel and create access sites for in-memory computations.

    • S. Kasra Tabatabaei
    • , Boya Wang
    •  & Olgica Milenkovic

  • Article
    | Open Access

    Developing cyanobacteria as CO2-neutral cell factories relies on the knowledge of the regulation mechanisms for growth and metabolism. Here, the authors develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803 and screens genes potentially affecting growth and L-lactate tolerance and production.

    • Lun Yao
    • , Kiyan Shabestary
    •  & Elton P. Hudson

  • Article
    | Open Access

    To model hepatocyte function accurately in vitro, it is necessary to generate and maintain a polarized epithelium. Here, the authors describe a protocol to generate polarized human pluripotent stem cell-derived hepatocyte-like cells (HLCs) to model enteric virus production and drug secretion in vitro.

    • Viet Loan Dao Thi
    • , Xianfang Wu
    •  & Charles M. Rice

  • Article
    | Open Access

    Acellular tissue engineered vessels functionalised with VEGF are coated with a layer of endothelial cells after in vivo implantation, but the source of the cells are unknown. Here the authors provide evidence that monocytes expressing VEGF receptors can transdifferentiate into endothelial cells via a macrophage intermediate.

    • Randall J. Smith Jr.
    • , Bita Nasiri
    •  & Stelios T. Andreadis

  • Article
    | Open Access

    Data-independent acquisition-mass spectrometry (MS) typically requires many preparatory MS runs to produce experiment-specific spectral libraries. Here, the authors show that empirical correction of in silico predicted spectral libraries enables efficient generation of high-quality experiment-specific libraries.

    • Brian C. Searle
    • , Kristian E. Swearingen
    •  & Mathias Wilhelm

  • Article
    | Open Access

    The spectra of light used by photosynthetic organisms are determined by their pigmentation colour palettes. Here Liu et al. show that a genetically-encoded chimera of light-harvesting proteins from plants and reaction centres from purple bacteria allows for polychromatic solar energy harvesting.

    • Juntai Liu
    • , Vincent M. Friebe
    •  & Michael R. Jones

  • Article
    | Open Access

    Aging involves gradual loss of tissue function, and transcription factor (TF) expression can ameliorate this in progeroid mice. Here the authors show that transient TF expression reverses age-associated epigenetic marks, inflammatory profiles and restores regenerative potential in naturally aged human cells.

    • Tapash Jay Sarkar
    • , Marco Quarta
    •  & Vittorio Sebastiano

  • Article
    | Open Access

    Field effect transistors based on graphene hold promise for sensing applications. Here, the authors report a millimeter-sized transistor based on deformed graphene as a biosensor that can detect nucleic acid molecules having detection limit of ~18 molecules of DNA in physiological buffer solution and ~600 molecules in human serum.

    • Michael Taeyoung Hwang
    • , Mohammad Heiranian
    •  & Rashid Bashir

  • Article
    | Open Access

    Whole-cell catalyst-based hydroxytyrosol production is low. Here, the authors increase the efficiency of its production in E. coli by de-bottlenecking two enzymatic steps catalyzed by monooxygenase and tyramine oxidase using structure-based enzyme redesign or in vivo-directed evolution with the aid of a newly developed biosensor.

    • Jun Yao
    • , Yang He
    •  & Shuang-Yan Tang

  • Article
    | Open Access

    Biosynthetic mechanism for the type 2 diabetes treatment drug acarbose is not fully revealed. Here, the authors show that shunt pathways and inefficient amino-deoxyhexose biosynthesis lead to 1-epi-valienol and valienol accumulation, and minimizing the flux to these shunt products can increase acarbose titer in Actinoplanes species.

    • Qinqin Zhao
    • , Yuchang Luo
    •  & Zixin Deng

  • Article
    | Open Access

    Genetic variation in natural populations could represent gene drive resistant alleles, preventing successful application for population management. Here the authors survey 1280 genomes from three mosquito species and concludes natural variation will not be detrimental to deploying gene drive technology.

    • Hanno Schmidt
    • , Travis C. Collier
    •  & Gregory C. Lanzaro

  • Article
    | Open Access

    Regeneration of corneal stroma has been a challenge due to its sophisticated structure and the easy transformation of the keratocyte. Here, the authors use a hydrogel reinforced with orthogonally aligned fibres and serum free medium to maintain keratocyte phenotype for the in vivo stromal regeneration.

    • Bin Kong
    • , Yun Chen
    •  & Shengli Mi

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