Biotechnology articles within Nature Communications

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  • Article
    | Open Access

    Anaerobic digesters play an important role in biodegradation. In the MiDAS 5 project, the authors use global 16S rRNA sequencing to expand the microbial reference database, improving taxonomic classification and revealing how environmental factors and geography shape microbial communities in anaerobic digesters.

    • Morten Kam Dahl Dueholm
    • , Kasper Skytte Andersen
    •  & Per Halkjær Nielsen
  • Article
    | Open Access

    Industrial bioethanol production is driven by ecological interactions within the microbial community rather than the interactions within yeast population. Here, the authors identify bacteria affecting ethanol production and reveal temperature as the major driving force for strain-level dynamics.

    • Felipe Senne de Oliveira Lino
    • , Shilpa Garg
    •  & Morten Otto Alexander Sommer
  • Article
    | Open Access

    It’s difficult to precisely modulate translation-level gene expression using CRISPR-dCas13 due to the lack of detailed characterization of the system. Here, the authors fill the knowledge gap and develop a synthetic tunable Tl-CRISPRi system to enable precise and predictable control of mRNA translation.

    • Giho Kim
    • , Ho Joon Kim
    •  & Sang Woo Seo
  • Article
    | Open Access

    Quantifying animal behavior is crucial in various fields such as neuroscience and ecology, yet we lack data-efficient methods to perform behavioral quantification. Here, the authors provide new unified models across 45+ species without manual labeling, thus enhancing analysis in behavioral studies.

    • Shaokai Ye
    • , Anastasiia Filippova
    •  & Mackenzie Weygandt Mathis
  • Article
    | Open Access

    ATP dynamics influence bioproduction yet are largely unexplored in this context. Here, authors unravel ATP dynamics across various conditions, identify carbon sources which boost ATP levels and bioproduction, and uncover metabolic bottlenecks, shedding light on how ATP dynamics can be used to enhance bioproduction.

    • Xinyue Mu
    • , Trent D. Evans
    •  & Fuzhong Zhang
  • Article
    | Open Access

    In this study, the authors show that nanovaccines co-delivering EBV antigens and molecular adjuvants generate high levels of neutralizing antibodies targeting vulnerable EBV sites of gHgL, gB and gp42. Antibodies elicited by cocktail nanovaccine immunization provide durable protection against EBV-associated lymphoma.

    • Ling Zhong
    • , Wanlin Zhang
    •  & Xiao Zhang
  • Article
    | Open Access

    mRNA therapeutics are revolutionizing the pharmaceutical industry. In this study, the authors characterize 5’UTR-regulated translation in cell types relevant for mRNA therapies and with fully random 5’UTRs, and show that 5’UTRs optimized via deep learning support high performance on mRNA-encoded gene editors.

    • Sebastian Castillo-Hair
    • , Stephen Fedak
    •  & Georg Seelig
  • Article
    | Open Access

    Enzymes of central metabolism tend to assemble into transient supramolecular complexes. Here, the authors stoichiometrically perturbed the supramolecular complex of TCA cycle enzymes in B. subtilis and propose that MDH-ICD clustering causes 2-oxoglutartae sequestration by reducing its diffusion rate, a mechanism that has evolved to regulate flux through the carbon-nitrogen metabolic branch-point.

    • Weronika Jasinska
    • , Mirco Dindo
    •  & Shimon Bershtein
  • Article
    | Open Access

    Single-cell RNA sequencing (scRNA-seq) is widely used to characterize cell types based on their average gene expression profiles, however most studies do not consider cell type-specific variation across individuals. Here the authors introduce a model to study cell type-specificity of inter-individual variation in scRNA-seq data and show that it can identify biologically meaningful signals missed by conventional differential expression tests.

    • Minhui Chen
    •  & Andy Dahl
  • Article
    | Open Access

    Technologies that generate precise combinatorial genome modifications are well suited to dissect the polygenic basis of complex phenotypes and engineer synthetic genomes. Here the authors systematically optimize eMAGE for enhanced editing efficiency and editing distance and apply these advances to identify genetic factors of nuclear hormone dysfunction.

    • Peter N. Ciaccia
    • , Zhuobin Liang
    •  & Farren J. Isaacs
  • Perspective
    | Open Access

    Organ on Chip platforms hold significant promise as alternatives to traditional animal models or cell cultures. In this Perspective, the authors examine the barriers that prevent widespread dissemination and deployment of these systems.

    • Charles G. Alver
    • , Emma Drabbe
    •  & Ashutosh Agarwal
  • Article
    | Open Access

    Hepatocellular carcinoma is the most common type of primary liver cancer. Here the authors show an oxygen gradient chip that separates aggressive hepatocellular carcinoma cells from a heterogeneous tumor mass, mirroring the conditions of the portal vein, hepatic artery, and liver.

    • Sewoom Baek
    • , Hyun-Su Ha
    •  & Hak-Joon Sung
  • Article
    | Open Access

    There is an increasing demand for high sample throughput beyond traditional analytical techniques. Here the authors show that Ultra-high throughput assays, based on the integration of Acoustic Ejection Mass Spectrometry (AEMS) and peptide immunocapture provide precise quantification of inflammation and SARS-CoV-2 proteins with 15x sample throughput compared to LC-MS.

    • Bart Van Puyvelde
    • , Christie L. Hunter
    •  & Jennifer E. Van Eyk
  • Article
    | Open Access

    Generating 3D bone cell networks in vitro that mimic the dynamic process during early bone formation is vital for creating in vitro models of bone development for disease modeling and drug testing, but remains challenging. Herein, the authors report a synthetic biodegradable microporous hydrogel for in vitro generation of functional human bone cell networks in 3D and microfluidic integration.

    • Doris Zauchner
    • , Monica Zippora Müller
    •  & Xiao-Hua Qin
  • Article
    | Open Access

    Primary human hepatocyte (PHH) transplantation could be an alternative to liver transplantation. Here, the authors use the mRNA-LNP platform to express growth factors in the liver in a controlled manner to drastically improve PHH engraftment, thus, reducing disease burden and enhancing overall liver function.

    • Anna R. Smith
    • , Fatima Rizvi
    •  & Valerie Gouon-Evans
  • Article
    | Open Access

    Unbiasedly benchmarking SRT computational methods remains a pressing challenge. Here, authors develop scCube, a simulation framework enabling scalable, reproducible, and unbiased generation of simulated SRT data, allowing researchers to benchmark and evaluate different methods.

    • Jingyang Qian
    • , Hudong Bao
    •  & Yiyu Cheng
  • Article
    | Open Access

    New technologies assay tissue slices for cell locations and molecular markers, aiding in the study of tissue cellular organisation. Here, authors develop an experimental design method to improve the cost-efficiency of spatial genomics experiments by iteratively selecting the most informative tissue slices.

    • Andrew Jones
    • , Diana Cai
    •  & Barbara E. Engelhardt
  • Article
    | Open Access

    Single-cell and spatial omics come with a trade-off between resolution and gene coverage. Here, authors bridge this gap via DOT, a multi-objective optimisation model for localising cell features in high/low-resolution spatial data considering cell composition, heterogeneity, and technical effects.

    • Arezou Rahimi
    • , Luis A. Vale-Silva
    •  & Julio Saez-Rodriguez
  • Article
    | Open Access

    Engineered sex ratio distorters have been proposed as a powerful component of genetic control strategies designed to suppress harmful insect pests. Here the authors show that sex ratio distorters behave in unexpected ways in malaria mosquitoes, offering new paths for genetic pest control by targeting sex ratios.

    • Daniella An Haber
    • , Yael Arien
    •  & Philippos Aris Papathanos
  • Article
    | Open Access

    Targeted gene delivery to the brain is a critical tool for neuroscience research and has significant potential to treat human disease. Here the authors engineer the protein shell of a common gene therapy vector for enhanced efficiency and specificity of brain delivery in ultrasound-targeted brain regions.

    • Hongyi R. Li
    • , Manwal Harb
    •  & Jerzy O. Szablowski
  • Article
    | Open Access

    Histidine kinases form part of bacterial two-component signaling systems (TCS). By modulating the balance between antagonistic kinase and phosphatase activities, the authors reprogram output and sensitivity of light-responsive TCSs, thus generating tools for gene-expression control by red light.

    • Stefanie S. M. Meier
    • , Elina Multamäki
    •  & Andreas Möglich
  • Article
    | Open Access

    Synthetic biology applications require finely tuned gene expression, often mediated by synthetic transcription factors. Here the authors validate two plant-derived proteins, FHY1 and FHL, acting as transactivators in mammalian cells for orthogonal, modular, and tunable control of gene transcription by forming a photosensing transcriptional regulation complex with PhyA.

    • Deqiang Kong
    • , Yang Zhou
    •  & Haifeng Ye
  • Article
    | Open Access

    Developing artificial leaves is crucial for advancing Net Zero Future, but most artificial leaves rely on the use of metal or semiconductors catalysts that usually have a lower catalytic activity and selectivity compared to biocatalysts. Here the AUs report Ecoleaf, a biodegradable artificial leaf that mimics the controlled expansion and contraction of stomata and enables enzymic CO2 conversion.

    • Xing Zhu
    • , Chenxi Du
    •  & Bin He
  • Article
    | Open Access

    Extracellular vesicles have been exploited as potential therapeutic agents. Here, the authors apply a nanovial technology to select sub-populations of cells that secrete high levels of extracellular vesicles, leading to improved therapeutic efficacy when delivered in vivo.

    • Doyeon Koo
    • , Xiao Cheng
    •  & Dino Di Carlo
  • Perspective
    | Open Access

    The way we generate and treat plastic waste is a key consideration in the transition from a take-make-waste model to a truly circular economy. Here, authors discuss their views on how biotechnology could contribute to solving the plastic problem, and the barriers we need to overcome to make such approaches a reality.

    • Amelia R. Bergeson
    • , Ashli J. Silvera
    •  & Hal S. Alper
  • Article
    | Open Access

    Bioadhesive materials and patches are promising alternatives to surgical sutures and staples but many existing bioadhesives do not meet the functional requirements of current surgical procedures. Here the authors present a tissue adhesive, stretchable and rapid photo-projection compatible translational patch material which is able to deliver therapeutics.

    • Parth Chansoria
    • , Ameya Chaudhari
    •  & Juliane Nguyen
  • Article
    | Open Access

    The mechanical properties of spider silk are a consequence of the structural organisation of proteins known as spidroins. Here the authors investigate the structure of the fibers formed by a C-terminal domain of a major spidroin: the study elucidates the mechanisms by which spidroins are transformed from soluble form into a fiber.

    • Danilo Hirabae De Oliveira
    • , Vasantha Gowda
    •  & My Hedhammar
  • Perspective
    | Open Access

    Microbial degradation and biosynthesis of fluorinated compounds is a field of increasing importance, but is hampered by the significant toxicity of fluoride. Here authors discuss emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms, providing guidance on how this knowledge can guide future bioengineering approaches.

    • Randy B. Stockbridge
    •  & Lawrence P. Wackett
  • Article
    | Open Access

    Human cervical mucosa and its interactions with the microbiome play a central role in female reproductive tract health and disease. Here, the authors develop physiological models of the human cervix using Organ-on-a-Chip technology that produce mucus, and respond to hormonal, environmental, and microbial cues similar to the living cervix.

    • Zohreh Izadifar
    • , Justin Cotton
    •  & Donald E. Ingber
  • Article
    | Open Access

    Molecular computing is an emerging paradigm with a crucial role in clinical diagnosis. Here, authors develop a spatially localized, DNA-integrated circuits-based classifier, DNA IC-CLA, which enables accurate cancer diagnosis for clinical samples in a faster and more effective manner.

    • Linlin Yang
    • , Qian Tang
    •  & Da Han
  • Article
    | Open Access

    Gene therapy is a rapidly growing field, but is hindered by efficacy and safety concerns, including those related to delivery methods. Here, inspired by the use of foam in the delivery of pharmaceuticals, Dr. Stephan and colleagues formulated foam as a safe and effective delivery platform for gene therapy.

    • K. Fitzgerald
    • , S. B. Stephan
    •  & M. T. Stephan
  • Article
    | Open Access

    It is difficult to detect low abundance RNAs in sequencing experiments, and biochemical methods to enrich or deplete specific RNAs are time-consuming, costly and can damage RNA. Here, authors develop a biochemical-free technology to enrich or deplete RNA classes in real-time during direct RNA sequencing.

    • Alexandra Sneddon
    • , Agin Ravindran
    •  & Eduardo Eyras
  • Article
    | Open Access

    Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here, the authors describe a platform to deliver defined numbers of macromolecules into cultured cell lines at single molecule resolution.

    • Chalmers C. Chau
    • , Christopher M. Maffeo
    •  & Paolo Actis
  • Article
    | Open Access

    Soluble methane monooxygenase (sMMO) is a potentially value biocatalyst, but production of active recombinant sMMO is very challenging. Here the authors report the rational design and construction of a catalytically active miniature sMMO which enables high-yield production of methanol in E. coli.

    • Yeonhwa Yu
    • , Yongfan Shi
    •  & Jeewon Lee
  • Review Article
    | Open Access

    This review explores the role of oxygen and its delivery via engineered biomaterials in a plethora of physiological processes. This piece emphasises on the application of advanced oxygen delivery strategies, as well as discussing advances in oxygen-generating materials and oxygen-perfusing devices.

    • Elizabeth Zoneff
    • , Yi Wang
    •  & Lilith M. Caballero-Aguilar
  • Article
    | Open Access

    Biotic-abiotic photosynthetic systems hold great promise to innovate solar-driven chemical transformation. Here, the authors construct a biotic-abiotic hybrid system composed of Shewanella oneidensis MR-1 and biogenic Se0 nanoparticles for photothermal Cu2-xSe biomineralization and then for seawater desalination.

    • Sheng-Lan Gong
    • , YangChao Tian
    •  & Li-Jiao Tian