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| Open AccessHighly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes
Leveraging the fact that eukaryotic genomes are organized into gene modules, FISHnCHIPs images multiple co-expressed genes simultaneously for sensitive and high throughput profiling of gene programs and cell types in tissues.
- Xinrui Zhou
- , Wan Yi Seow
- & Kok Hao Chen
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Article
| Open AccessEdible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit
Fungi have the potential to produce sustainable foods for a growing population, but current products are based on a small number of strains with inherent limitations. Here, the authors develop genetic tools for an edible fungus and engineer its nutritional value and sensory appeal for alternative meat applications.
- Vayu Maini Rekdal
- , Casper R. B. van der Luijt
- & Jay D. Keasling
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Article
| Open AccessThunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are targets for developing vaccines and immunotherapies. Here the authors report Thunder-DDA-PASEF, an immunopeptidomics method which enhances the identification of vital HLAIps crucial for vaccine and immunotherapy development.
- David Gomez-Zepeda
- , Danielle Arnold-Schild
- & Stefan Tenzer
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Article
| Open AccessNanobubble-actuated ultrasound neuromodulation for selectively shaping behavior in mice
Ultrasound may be used to non-invasively modulate the brain. Here the authors describe acoustic nanobubble-mediated ultrasound stimulation of specific brain region in male mice.
- Xuandi Hou
- , Jianing Jing
- & Lei Sun
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Article
| Open AccessIdentifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer. Here, authors develop a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation programs, showing that SMARCB1 restricts differentiation, and nominating other regulators with therapeutic potential.
- Sandor Spisak
- , David Chen
- & Nilay S. Sethi
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Article
| Open AccessInhalation of ACE2-expressing lung exosomes provides prophylactic protection against SARS-CoV-2
Inhibiting SARS-CoV-2 interaction with ACE2 is a promising antiviral strategy. Here, the authors show that exosomes derived from human lung spheroid cells expressing hACE2 accumulate in the lung following prophylactic inhalation to bind and neutralize SARS-CoV-2 and protect mice from SARS-CoV-2-induced disease.
- Zhenzhen Wang
- , Shiqi Hu
- & Ke Cheng
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Article
| Open AccessSynapsin 2a tetramerisation selectively controls the presynaptic nanoscale organisation of reserve synaptic vesicles
How synaptic vesicles (SVs) are clustered at the presynapse is suggestive of anchoring processes counteracting their diffusion. Here, the authors co-track recycling and reserve SVs in live neurons to find that Synapsin 2a tetramerization dynamically immobilizes reserve SVs at the presynapse.
- Shanley F. Longfield
- , Rachel S. Gormal
- & Frédéric A. Meunier
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Article
| Open AccessIdentification of four biotypes in temporal lobe epilepsy via machine learning on brain images
Brain imaging-based disease progression modelling is a promising technique for disease stratification. Here the authors characterize distinct ‘trajectories’ of brain atrophy in temporal lobe epilepsy and identify four subtypes with distinct neuroanatomical signatures.
- Yuchao Jiang
- , Wei Li
- & Dongmei An
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Article
| Open AccessSingle-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung
This study uses single-cell transcriptomics to examine how lung cells respond to targeted damage. The authors employ genetically modified mouse models and cell sorting to enrich for rare, actively dividing cells, revealing cell types/states and alternative differentiation paths.
- Leila R. Martins
- , Lina Sieverling
- & Claudia Scholl
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Article
| Open AccessPHEIGES: all-cell-free phage synthesis and selection from engineered genomes
Bacteriophages have great potential in both medicine and biotechnology. Here the authors present PHEIGES, a cell-free method for phage genome engineering, synthesis and selection based on T7, which allows direct selection of engineered and mutant phages without compartmentalization.
- Antoine Levrier
- , Ioannis Karpathakis
- & Vincent Noireaux
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Article
| Open AccessdCas13-mediated translational repression for accurate gene silencing in mammalian cells
Current gene silencing tools can have drawbacks. Here the authors report CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13): they also show that fusion of a translational repressor to dCas13 further improved the performance.
- Antonios Apostolopoulos
- , Naohiro Kawamoto
- & Shintaro Iwasaki
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Article
| Open AccessSimultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions
Protein function depends on their subcellular location and turnover rate. Here, the authors report a method to measure spatial and temporal proteome dynamics simultaneously, revealing compartment-specific protein turnover and translocation in cardiac cells under ER stress and carfilzomib treatment.
- Jordan Currie
- , Vyshnavi Manda
- & Edward Lau
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Article
| Open AccessAn organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome
Endocrinologists have traditionally focused on studying one hormone or organ system at a time. Here the authors use transcriptomic data from the mouse lemur to globally characterize primate hormonal signaling, describing hormone sources and targets, identifying conserved and primate specific regulation, and elucidating principles of the network.
- Shixuan Liu
- , Camille Ezran
- & James E. Ferrell Jr.
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Article
| Open AccessTissue engineered vascular grafts are resistant to the formation of dystrophic calcification
Advancements in congenital heart surgery stress the need for durable biomaterials. Here, the authors compare tissue-engineered vascular grafts (TEVGs) with traditional polytetrafluoroethylene grafts, revealing TEVGs’ superior durability and reduced calcification, promising improved long-term success for surgeries.
- Mackenzie E. Turner
- , Kevin M. Blum
- & Christopher K. Breuer
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Article
| Open AccessInterrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance
RNA splicing serves as a critical layer of gene expression regulation. Here, authors introduce SCASL for investigating the heterogeneity of RNA splicing landscapes at single-cell resolution, offering a novel scheme for classifying cell identities with physiological relevance.
- Xianke Xiang
- , Yao He
- & Xuerui Yang
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Article
| Open AccessDesymmetric homologating annulation to access chiral pentafulvenes and their application in bioimaging
Polycyclic/multisubstituted pentafulvenes are of interest as they frequently occur in biologically relevant motifs, electrochromic dyes, and solar cells. Here, the authors report an enantioselective homologating annulation of cyclopent-4-ene-dione with 3-cyano-4-methylcoumarins through L-tert-leucine derived thiourea catalysis, affording a wide range of enantioenriched polycyclic multi-substituted embedded aminopentafulvenes.
- Sanjay Singh
- , Ravi Saini
- & Ravi P. Singh
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Article
| Open AccessProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs
Identifying small proteins is challenging. ProTInSeq uses modified transposons to express markers inserted in-frame to protein-coding genes. This method identifies 153 unannotated small proteins in M. pneumoniae and additional proteomic information.
- Samuel Miravet-Verde
- , Rocco Mazzolini
- & Luis Serrano
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Article
| Open AccessBioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2
The main protease (Mpro) plays a crucial role in the replication of SARS-CoV-2, thereby making it an attractive target for COVID-19 treatment. Here, the authors develop a colorimetric screening platform for discovering Mpro inhibitors using engineered amyloid peptide-based nanocomplexes.
- Dongtak Lee
- , Hyo Gi Jung
- & Dae Sung Yoon
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Article
| Open AccessCas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements
Engineered biosensing bacteria can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. Here the authors present a robust biocontainment assisted by Cas9 and an engineered gene expression control combined in a genetically engineered human commensal bacterium that successfully functioned in a mouse intestinal tract as well as cell culture condition.
- Naoki Hayashi
- , Yong Lai
- & Timothy K. Lu
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Article
| Open AccessKdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons
Kdm1a is a histone demethylase implicated in intellectual disability. Here, the authors show that removing Kdm1a in neurons of the adult mouse forebrain disrupts silencing of nonneuronal genes and chromatin organization, emphasizing its role in preserving neuronal genome integrity.
- Beatriz del Blanco
- , Sergio Niñerola
- & Ángel Barco
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Article
| Open AccessGene expression analyses reveal differences in children’s response to malaria according to their age
Here the authors use dual RNA sequencing to characterize host and parasite gene expression from 136 Malian children with symptomatic Plasmodium falciparum infection. They find that parasitemia levels correlate with neutrophil and T cell levels and that the child’s age correlates with innate immune gene expression as well as gametocyte levels.
- Kieran Tebben
- , Salif Yirampo
- & David Serre
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Article
| Open AccessAn artificial protein modulator reprogramming neuronal protein functions
Direct modulation of protein by artificial catalysts as enzyme mimetics remains hindered by the lack of highly efficient catalytic centers. Here, the authors present the development of artificial protein modulators (APROMs) with protein phosphatase-like characteristics, catalytically reprogram the biological function of α-synuclein.
- Peihua Lin
- , Bo Zhang
- & Daishun Ling
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Article
| Open AccessEndogenous stimuli-responsive separating microneedles to inhibit hypertrophic scar through remodeling the pathological microenvironment
The treatment of hypertrophic scar (HS) is hindered by the low bioavailability of drugs and the pathological microenvironment. Here the authors report a separating microneedle drug delivery system responsive to high reactive oxygen species levels and overexpression of matrix metalloproteinases to remodel the pathological microenvironment for HS treatment.
- Zhuo-Ran Yang
- , Huinan Suo
- & Jintao Zhu
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Article
| Open AccessA single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification
Studying Drosophila trachea development can inform the mechanisms of growth of all tubular structures. Here, the authors generate a transcriptomic cell atlas of the developing fly trachea and establish roles for Notch signaling, which may be disrupted by diet-induced glycosylation.
- Yue Li
- , Tianfeng Lu
- & Hai Huang
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Article
| Open AccessMachine learning-aided design and screening of an emergent protein function in synthetic cells
Here, the authors introduce a pipeline to screen machine learning generated variants of a protein that forms intracellular spatiotemporal patterns in E. coli, demonstrating the best variants can substitute the wildtype gene.
- Shunshi Kohyama
- , Béla P. Frohn
- & Petra Schwille
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Article
| Open AccessNanopore analysis of salvianolic acids in herbal medicines
Natural herbs, which contain pharmacologically active compounds, have been historically used as medicines but the analysis of their chemical components is time-consuming and complex. Here, the authors report a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore for sensing a variety of bioactive compounds based on salvianolic acid, without the need for sample separation or purification.
- Pingping Fan
- , Shanyu Zhang
- & Shuo Huang
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Article
| Open AccessRiboformer: a deep learning framework for predicting context-dependent translation dynamics
Riboformer is a deep learning-based framework that predicts changes in translation dynamics with codon-level precision. It corrects experimental artifacts in ribosome profiling data and identifies sequences causing ribosome stalling.
- Bin Shao
- , Jiawei Yan
- & Allen R. Buskirk
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Article
| Open AccessSpecific pharmacological and Gi/o protein responses of some native GPCRs in neurons
G protein responses mediated by GPCRs may differ depending on their environment. Here, using highly sensitive Gi/o sensors, the authors reveal the specific pharmacological and Gi/o protein responses of some native GPCRs in neurons, and the influence of G protein composition.
- Chanjuan Xu
- , Yiwei Zhou
- & Jianfeng Liu
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Article
| Open AccessNeuronal miR-9 promotes HSV-1 epigenetic silencing and latency by repressing Oct-1 and Onecut family genes
Here, the authors identify neuron-specific miR-9 that potentially blocks HSV-1 neuronal replication by targeting host OCT-1 and ONECUT transcription factors involved in epigenetic activation of HSV-1 productive-cycle genes. Thus miR-9 promotes viral epigenetic silencing and latent infection in neurons.
- Yue Deng
- , Yuqi Lin
- & Dongli Pan
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Article
| Open AccessLight-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis
Current imaging flow cytometry approaches remain limited in their ability to reveal subcellular information with high-resolution and instrumental simplicity. Here, the authors present a light-field flow cytometer capable of high-content, multi-color imaging of cells with high-resolution in 3D.
- Xuanwen Hua
- , Keyi Han
- & Shu Jia
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Article
| Open AccessA humanized mouse model for adeno-associated viral gene therapy
All natural AAV serotypes transduce murine hepatocytes more efficiently than their human counterparts in human liver chimeric mouse models. Here the authors developed a novel humanized mouse were human transduction of AAV can be studied.
- Mercedes Barzi
- , Tong Chen
- & Karl-Dimiter Bissig
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Article
| Open AccessPolycomb-mediated silencing of miR-8 is required for maintenance of intestinal stemness in Drosophila melanogaster
Intestinal physiology requires a balance between stem cell self-renewal and differentiation. Here, the authors show that this balance is regulated epigenetically by a dynamic relationship between the evolutionarily conserved PRC2, miR-8 and Notch signaling.
- Zoe Veneti
- , Virginia Fasoulaki
- & Aristides G. Eliopoulos
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Article
| Open AccessDistinct neurochemical influences on fMRI response polarity in the striatum
The relationship between striatal vascular and neural activity is not fully understood. Here the authors found neuronal activity inadequately explains striatal hemodynamic polarity, challenging classic fMRI interpretations.
- Domenic H. Cerri
- , Daniel L. Albaugh
- & Yen-Yu Ian Shih
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Article
| Open AccessCryo-EM structure of cell-free synthesized human histamine 2 receptor/Gs complex in nanodisc environment
The study describes the molecular structure of the human histamine 2 receptor in active conformation and in complex with Gs heterotrimer, synthesized in a cell-free system and co-translationally inserted into preformed nanodiscs.
- Zoe Köck
- , Kilian Schnelle
- & Frank Bernhard
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Article
| Open AccessMirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins
Mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders but is hindered by the optimization required for D-protein chemical synthesis. Here, the authors report a general mirror-image phage display pipeline based on automated flow peptide synthesis and use it to prepare and characterize 12 L/D-protein pairs.
- Alex J. Callahan
- , Satish Gandhesiri
- & Bradley L. Pentelute
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Article
| Open AccessscCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells
Extrachromosomal circular DNAs (eccDNAs) affect gene expression and tumour progression. Here, the authors report a method, scCircle-seq, for eccDNA profiling in single cells, demonstrating the stochasticity, cell type specificity, and dynamics of eccDNAs in cell lines and primary tumour samples.
- Jinxin Phaedo Chen
- , Constantin Diekmann
- & Nicola Crosetto
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Article
| Open AccessMeasuring sub-nanometer undulations at microsecond temporal resolution with metal- and graphene-induced energy transfer spectroscopy
Studying the fluctuations of biological membranes with high resolution is challenging. Here, the authors combine metal- and graphene-induced energy transfer (MIET/GIET) with fluorescence correlation spectroscopy (FCS) to monitor such fluctuations with nanometer and microsecond resolution.
- Tao Chen
- , Narain Karedla
- & Jörg Enderlein
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Article
| Open AccessAutomatic data-driven design and 3D printing of custom ocular prostheses
Manual processes to produce ocular prostheses are time-consuming and yield varying quality. Here, authors present an automatic digital end-to-end process for custom ocular prostheses. It creates shape and appearance from image data of an OCT device and produces them using a full-colour 3D printer.
- Johann Reinhard
- , Philipp Urban
- & Mandeep S. Sagoo
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Article
| Open AccessEngineering self-deliverable ribonucleoproteins for genome editing in the brain
The delivery of CRISPR RNPs has potential advantages over other genome editing approaches, including reduced off-target editing and reduced immunogenicity. Here the authors report self-deliverable Cas9 RNPs capable of robustly editing cultured cells in vitro and the mouse brain upon direct injections.
- Kai Chen
- , Elizabeth C. Stahl
- & Jennifer A. Doudna
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Article
| Open AccessDeciphering the mechanism of glutaredoxin-catalyzed roGFP2 redox sensing reveals a ternary complex with glutathione for protein disulfide reduction
Fusion proteins between roGFP2 and glutaredoxins are used for intracellular redox measurements. Here, the authors determined all rate constants of the reaction cycle for roGFP2 measurements and identified an alternative glutaredoxin mechanism.
- Fabian Geissel
- , Lukas Lang
- & Marcel Deponte
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Article
| Open AccessNucleocapsid protein-specific monoclonal antibodies protect mice against Crimean-Congo hemorrhagic fever virus
There are limited treatment options for infection with Crimean-Congo hemorrhagic fever virus in humans. Here, the authors show that a monoclonal antibody targeting the highly conserved viral nucleocapsid protein provides protective effects in a mouse model of infection.
- Aura R. Garrison
- , Vanessa Moresco
- & Joseph W. Golden
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Article
| Open AccessMarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution
Three-dimensional analysis of the intact bone marrow within whole long bones remains very challenging. Here, the authors present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur.
- Till Fabian Mertens
- , Alina Tabea Liebheit
- & Anja Erika Hauser
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Article
| Open AccessSEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis
There is a lack of universal tools to analyse protein assemblies and quantify underlying structures in single-molecule localization microscopy. Here, the authors present SEMORE, a semi-automatic machine learning framework for system- and input-dependent analysis of super-resolution data.
- Steen W. B. Bender
- , Marcus W. Dreisler
- & Nikos S. Hatzakis
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Article
| Open AccessT-DOpE probes reveal sensitivity of hippocampal oscillations to cannabinoids in behaving mice
Neural activity is regulated by synapse-neuromodulator interactions, necessitating optoelectro-pharmacological investigations. Here, authors implement their multi-modal probe to show focal infusion of synthetic cannabinoid disrupts CA1 oscillations.
- Jongwoon Kim
- , Hengji Huang
- & Xiaoting Jia
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Article
| Open AccessPhage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference
Existing TadA-derived CBEs exhibit residual A•T-to-G•C editing activity and suffer from lower activity at several sequence contexts and with non-SpCas9 targeting domains. Here, the authors use phage-assisted evolution to evolve CBE6 variants that address these limitations.
- Emily Zhang
- , Monica E. Neugebauer
- & David R. Liu
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Article
| Open AccessSingle-molecule RNA sizing enables quantitative analysis of alternative transcription termination
The development of RNA technologies demands accurate assessment of transcript size and heterogeneity. Here, authors report a nanopore-based approach to study full-length RNA transcripts at the single-molecule level, identify premature transcription termination and study rolling-circle transcription.
- Gerardo Patiño-Guillén
- , Jovan Pešović
- & Ulrich Felix Keyser
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Article
| Open AccessVirtual histological staining of unlabeled autopsy tissue
Conventional staining of post-mortem samples can be affected by several factors, including tissue autolysis. Here, the authors demonstrate a virtual staining tool using a trained neural network to turn autofluorescence images of label-free autopsy tissue into brightfield equivalent images.
- Yuzhu Li
- , Nir Pillar
- & Aydogan Ozcan
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Article
| Open AccessMotility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle
Inspired by biology, great progress has been made in creating artificial molecular motors. Here the authors report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor and show their design is capable of track-guided motion.
- Chapin S. Korosec
- , Ivan N. Unksov
- & Nancy R. Forde
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Article
| Open AccessProtein design using structure-based residue preferences
Recent protein design methods rely on large neural networks, yet it is unclear which dependencies are critical for determining function. Here, authors show that learning the per residue mutation preferences, without considering interactions, enables design of functional and diverse protein variants.
- David Ding
- , Ada Y. Shaw
- & Debora S. Marks
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