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programmable polyketide biosynthesis platform for production of aromatic compounds in yeast

Synthetic and Systems Biotechnology 2020年第1期5卷 11-18页

作者： Tadas Jakočiūnas Andreas K.Klitgaard Eftychia Eva Kontou Julie Bang Nielsen Emil Thomsen David Romero-Suarez Kai Blin Christopher J.Petzold Jennifer W.Gin Yaojun Tong Charlotte Held Gotfredsen Pep Charusanti Rasmus J.N.Frandsen Tilmann Weber Sang Yup Lee Michael K.Jensen Jay D.Keasling The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKgs.LyngbyDenmark Joint BioEnergy Institute EmeryvilleCAUSA Biological Systems&Engineering Division Lawrence Berkeley National LaboratoryBerkeleyCAUSA Department of Chemical and Biomolecular Engineering&Department of Bioengineering University of California BerkeleyCAUSA Center for Synthetic Biochemistry Institute for Synthetic BiologyShenzhen Institutes for Advanced TechnologiesShenzhenChina Department of Chemistry Technical University of DenmarkKgs.LyngbyDenmark Department of Biotechnology and Biomedicine Technical University of DenmarkKgs.LyngbyDenmark Department of Chemical and Biomolecular Engineering(BK21 Plus Program) Korea Advanced Institute of Science and Technology(KAIST)291 Daehak-roYuseong-guDaejeon34141Republic of Korea

To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms,development of new,versatile,bio-based production platforms is *** we present a novel yeast-based platform for biosynthesis of bacterial aromatic *** platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.

关键词： Natural products Synthetic biology Aromatic polyketides CRISPR/Cas9 Polyketide Production platform in eukaryotes Metabolic engineering Biotechnology

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Erratum: Bok's equi-volume principle: Translation, historical context, and a modern perspective

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Brain Multiphysics 2024年 7卷

作者： Jack Consolini Nagehan Demirci Andrew Fulwider Jeffrey J. Hutsler Maria A. Holland Department of Aerospace and Mechanical Engineering University of Notre Dame Notre Dame IN 46556 USA Bioengineering Graduate Program University of Notre Dame Notre Dame IN 46556 USA Department of Chemical and Biomolecular Engineering University of Notre Dame Notre Dame IN 46556 USA Department of German and Russian Languages and Literatures University of Notre Dame Notre Dame IN 46556 USA Program in Neuroscience University of Nevada Reno NV 89557 USA

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Corrigendum to "Tissue-adhesive hydrogel for multimodal drug release to immune cells in skin" [Acta Biomaterialia Volume 150, Pages 211-220]

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Acta biomaterialia 2024年 179卷 398页

作者： Nicole B Day Rianne Dalhuisen Nichole E Loomis Sarah G Adzema Jai Prakash C Wyatt Shields Department of Chemical and Biological Engineering University of Colorado Boulder Boulder CO 80303 United States. Department of Chemical and Biological Engineering University of Colorado Boulder Boulder CO 80303 United States Department of Advanced Organ Bioengineering and Therapeutics Section: Engineered Therapeutics University of Twente Enschede the Netherlands. Biomedical Engineering Program University of Colorado Boulder Boulder CO 80303 United States. Electronic address: Charles.Shields@colorado.edu.

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A call to action to address escalating global threats to academic research

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The Innovation 2025年第4期6卷 17-19页

作者： Gaelle Piret Fun Man Fung Josie Fullerton Giuseppe Fico Dmitriy Ponkratov Wenxin Chen Daniela Latorre Kirsty Y.Wan Nima Aghaeepour Jules Welgryn Adeel Razi Patricia Silveyra Ahmet Altun Renata Z.Jurkowska Alice C.Hughes Joy Wolfram INSERM U1205 UGA38400 Saint Martin d’HèresFrance School of Chemistry University College DublinD04 C1P1 BelfieldIreland UCD Geary Institute for Public Policy University College DublinD04 N9Y1 DublinIreland School of Cardiovascular&Metabolic Health University of GlasgowG128TA GlasgowUK European Alliance for Medical and Biological Engineering and Science 3001 LeuvenBelgium Life Supporting Technologies Universidad Politécnica de Madrid28040 MadridSpain Siemens Digital Industries Software B908BG SolihullUK Department of Philosophy of Science and Technology University of Science and Technology of ChinaHefei 230026China Institute of Microbiology ETH Zurich8093 ZurichSwitzerland Living Systems Institute&Department of Mathematics and Statistics University of ExeterEX44QD ExeterUK Department of Anesthesiology Painand Perioperative MedicineDepartment of PediatricsDepartment of Biomedical Data ScienceStanford University School of MedicineStanfordCA 94305USA UniversitéParis Nanterre 92000 NanterreFrance Turner Institute for Brain and Mental Health School of Psychological Sciencesand Monash Biomedical ImagingMonash UniversityClaytonVIC 3800Australia Wellcome Centre for Human Neuroimaging University College LondonWC1N 3AR LondonUK CIFAR Azrieli Global Scholars Program TorontoON M5G 1M1Canada Department of Environmental and Occupational Health Indiana University School of Public Health BloomingtonBloomingtonIN 47408USA Department of Pharmacology Sivas Cumhuriyet UniversitySivas 58140Turkey Division of Biomedicine School of BiosciencesCardiff UniversityCF103AX CardiffUK School of Biological Sciences University of Hong KongHong Kong SAR 999077China Australian Institute for Bioengineering and Nanotechnology The University of QueenslandBrisbaneQLD 4072Australia School of Chemical Engineering The University of QueenslandBrisbaneQLD 4072Australia

This article is a call to action to address escalating threats to scientific progress that affect academic researchers across the *** threats include public mistrust of science,challenges in translating academic research to end-user applications,a disconnect between academics and policymakers,emerging barriers to international collaboration,and a reliance on conventional metrics to evaluate academic *** article presents various calls to action informed by exemplary approaches across the globe that serve as frameworks to drive beneficial transformation for researchers,academic institutions,and society.

关键词： academic research calls action global threats public mistrust sciencechallenges translating academic research disconnect academics policymakers call action translation research

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Diamine Surface Passivation and Post-Annealing Enhance Performance of Silicon-Perovskite Tandem Solar Cells

arXiv

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arXiv 2024年

作者： Taddei, Margherita Contreras, Hannah Doan, Hai-Nam McCarthy, Declan P. Seo, Seongrok Westbrook, Robert J.E. Graham, Daniel J. Datta, Kunal Carroy, Perrine Muñoz, Delfina Correa-Baena, Juan-Pablo Barlow, Stephen Marder, Seth R. Smith, Joel A. Snaith, Henry J. Ginger, David S. Department of Chemistry University of Washington SeattleWA98195 United States Department of Physics University of Oxford OxfordOX1 3PU United Kingdom Institute of Materials Science Technical University of Munich München85748 Germany Department of Chemistry University of Colorado-Boulder BoulderCO80309 United States Department of Bioengineering University of Washington SeattleWA98195 United States School of Materials Science and Engineering Georgia Institute of Technology North Ave NW AtlantaGA30332 United States Université Grenoble Alpes CEA Liten Campus Ines Le Bourget du Lac73375 France Renewable and Sustainable Energy Institute University of Colorado-Boulder BoulderCO80309 United States Department of Chemical and Biological Engineering and Materials Science Program University of Colorado-Boulder BoulderCO80309 United States Physical Sciences Division Physical and Computational Sciences Directorate Pacific Northwest National Laboratory RichlandWA99352 United States

We show that the use of 1,3-diaminopropane (DAP) as a chemical modifier at the perovskite/electron-transport layer (ETL) interface enhances the power conversion efficiency (PCE) of 1.7 eV bandgap FACs mixed-halide perovskite single-junction cells, primarily by boosting the open-circuit voltage (VOC) from 1.06 V to 1.15 V. Adding a post-processing annealing step after C60 evaporation, further improves the fill factor (FF) by 20% from the control to the DAP + post-annealing devices. Using hyperspectral photoluminescence microscopy, we demonstrate that annealing helps improve compositional homogeneity at the top and bottom interfaces of the solar cell, which prevents detrimental bandgap pinning in the devices and improves C60 adhesion. Using time-of-flight secondary ion mass spectrometry, we show that DAP reacts with formamidinium present near the surface of the perovskite lattice to form a larger molecular cation, 1,4,5,6-tetrahydropyrimidinium (THP) that remains at the interface. Combining the use of DAP and the annealing of C60 interface, we fabricate Si-perovskite tandems with PCE of 25.29%, compared to 23.26% for control devices. Our study underscores the critical role of chemical reactivity and thermal post-processing of the C60/Lewis-base passivator interface in minimizing device losses and advancing solar-cell performance of wide-bandgap mixed-cation mixed-halide perovskite for tandem application. © 2024, CC BY.

关键词： Perovskite

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Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates

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Cell 2025年

作者： Yan, Xiao Kuster, David Mohanty, Priyesh Nijssen, Jik Pombo-García, Karina Garcia Morato, Jorge Rizuan, Azamat Franzmann, Titus M. Sergeeva, Aleksandra Ly, Anh M. Liu, Feilin Passos, Patricia M. George, Leah Wang, Szu-Huan Shenoy, Jayakrishna Danielson, Helen L. Ozguney, Busra Honigmann, Alf Ayala, Yuna M. Fawzi, Nicolas L. Dickson, Dennis W. Rossoll, Wilfried Mittal, Jeetain Alberti, Simon Hyman, Anthony A. Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) Saxony Dresden 01307 Germany Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering Technische Universität Dresden Saxony Dresden 01307 Germany Artie McFerrin Department of Chemical Engineering Texas A&M University College Station 77843 TX United States Edward Doisy Department of Biochemistry and Molecular Biology Saint Louis University St. Louis 63104 MO United States Department of Molecular Biology Cell Biology & Biochemistry Brown University Providence 02912 RI United States Center for Biomedical Engineering Brown University Providence 02912 RI United States Department of Chemistry Texas A&M University College Station 77843 TX United States Interdisciplinary Graduate Program in Genetics and Genomics Texas A&M University College Station 77843 TX United States Department of Neuroscience Mayo Clinic Jacksonville 32224 FL United States

Cytosolic aggregation of the nuclear protein TAR DNA-binding protein 43 (TDP-43) is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43-enriched phase within stress granules, which subsequently transition into pathological aggregates. Intra-condensate demixing of TDP-43 is observed in iPS-motor neurons, a disease mouse model, and patient samples. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We suggest that up-concentration inside condensates followed by intra-condensate demixing could be a general pathway for protein aggregation. © 2025 The Author(s)

关键词： ALS biomolecular condensate FTD intra-condensate demixing neurodegenerative diseases oxidative stress phase separation protein aggregation stress granules TDP-43

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Bottom-up Biomaterial strategies for creating tailored stem cells in regenerative medicine

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Frontiers in bioengineering and biotechnology 2025年 13卷 1581292页

作者： Brenda Cruz-Gonzalez Ellie Johandes Dominique Gramm Donny Hanjaya-Putra Department of Aerospace and Mechanical Engineering Bioengineering Graduate Program University of Notre Dame Notre Dame IN United States. Harper Cancer Research Institute University of Notre Dame Notre Dame IN United States. Department of Chemical and Biomolecular Engineering University of Notre Dame Notre Dame IN United States. Center for Stem Cells and Regenerative Medicine University of Notre Dame Notre Dame IN United States.

Biomaterial-assisted stem cell therapies hold immense promise for regenerative medicine, yet clinical translation remains challenging. This review focuses on recent advances and persistent limitations in applying induced pluripotent stem cells (iPSCs), endothelial colony-forming cells (ECFCs), multipotent mesenchymal stromal cells (MSCs), and embryonic stem cells (ESCs) within engineered microenvironments. We introduce a novel "bottom-up" approach to biomaterial design. This approach focuses first on understanding the fundamental biological properties and microenvironmental needs of stem cells, then engineering cell-instructive biomaterials to support them. Unlike conventional methods that adapt cells to pre-existing materials, this strategy prioritizes designing biomaterials from the molecular level upward to address key challenges, including differentiation variability, incomplete matching of iPSCs to somatic counterparts, functional maturity of derived cells, and survival of ECFCs/MSCs in therapeutic niches. By replicating lineage-specific mechanical, chemical, and spatial cues, these tailored biomaterials enhance differentiation fidelity, reprogramming efficiency, and functional integration. This paradigm shift from passive scaffolds to dynamic, cell-instructive platforms bridges critical gaps between laboratory success and clinical translation, offering a transformative roadmap for regenerative medicine and tissue engineering.

关键词： 3D printing backpack molecules biomaterials disease modeling drug screening nanoparticles stem cells tissue engineerings

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Corrigendum to “Scaling iPSC production in different 3D platforms in suspension culture for their use in allogeneic regenerative therapies” [Biochem. Eng. J. 217 (2025) 109672]

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Biochemical engineering Journal 2025年 218卷

作者： Danton Freire-Flores Nyna Kawles Pablo Caviedes Barbara A. Andrews Juan A. Asenjo Centre for Biotechnology and Bioengineering Faculty of Physical and Mathematical Sciences Universidad de Chile Beaucheff 851 Santiago 8370448 Chile Department of Chemical Engineering Biotechnology and Materials Universidad de Chile Beaucheff 851 Santiago 8370448 Chile Program of Molecular and Clinical Pharmacology ICBM Faculty of Medicine University of Chile Independencia 1027 Santiago 8379482 Chile

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Imaging neurotransmitter transport in live cells with stimulated Raman scattering microscopy

arXiv

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arXiv 2022年

作者： Manifold, Bryce Dorlhiac, Gabriel F. Landry, Markita P. Streets, Aaron Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Biophysics Graduate Group University of California Berkeley BerkeleyCA94720 United States Department of Chemical and Biomolecular Engineering University of California Berkeley BerkeleyCA94720 United States Innovative Genomics Institute University of California Berkeley BerkeleyCA94720 United States California Institute for Quantitative Biosciences QB3 University of California Berkeley BerkeleyCA94720 United States Chan-Zuckerberg Biohub San FranciscoCA94158 United States UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California Berkeley BerkeleyCA94720 United States

chemical neurotransmission is central to neurotypical brain function but also implicated in a variety of psychiatric and neurodegenerative diseases. The release dynamics of neurotransmitters is correlated with but distinct from neuronal electrical signal propagation. It is therefore necessary to track neurotransmitter modulation separately from neuron electrical activity. Here, we present a new approach for imaging deuterated neurotransmitter molecules in the cell-silent window with stimulated Raman scattering (SRS) microscopy. Using SRS microscopy, we perform direct imaging of deuterated dopamine and GABA in PC12 chromaffin cells, and in primary hippocampal neurons, respectively, based on the carbon-deuterium vibrational frequencies. We demonstrate that SRS imaging of these isotopologues directly visualizes intracellular neurotransmitters without changing the neurotransmitters’ chemical identity, and requiring custom synthesis or genetic encoding protocols. We further show that stimulation of neurotransmitter release results in an overall 20-50% intracellular neurotransmitter signal reduction in agreement with comparable neurotransmission dynamics studies, with the ability to observe inter- and intracellular variation in vesicular neurotransmitter release. Taken together, our data suggest that neurotransmitter isotopologues can serve as a commercially-available, biocompatible, and generalizable method to image neurotransmitters with deuterated molecules that are virtually chemically identical to their native counterparts. © 2022, CC BY.

关键词： Stimulated Raman scattering

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Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

arXiv

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arXiv 2023年

作者： Takaba, Kenichiro Pulido, Iván Behara, Pavan Kumar Cavender, Chapin E. Friedman, Anika J. Henry, Michael M. MacDermott-Opeskin, Hugo Iacovella, Christopher R. Nagle, Arnav M. Payne, Alexander Matthew Shirts, Michael R. Mobley, David L. Chodera, John D. Wang, Yuanqing Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Pharmaceuticals Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Center for Neurotherapeutics Department of Pathology and Laboratory Medicine University of California IrvineCA92697 United States Skaggs School of Pharmacy and Pharmaceutical Sciences University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States Department of Chemical and Biological Engineering University of Colorado Boulder BoulderCO80309 United States Open Molecular Software Foundation DavisCA95618 United States Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Department of Pharmaceutical Sciences University of California IrvineCA92697 United States Tri-Institutional Ph.D. Program in Chemical Biology Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University New YorkNY10004 United States

The development of reliable and extensible molecular mechanics (MM) force fields—fast, empirical models characterizing the potential energy surface of molecular systems—is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest. © 2023, CC BY.

关键词： Quantum chemistry

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