1
|
Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024:10.1038/s41559-024-02353-4. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
Collapse
Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | | |
Collapse
|
2
|
Zhu Q, Zhao Q, Huang Q, Chen Y, Suresh S, Yang W, Zhang Z, Zhou H, Gao H, Wang J. Grain boundary plasticity initiated by excess volume. Proc Natl Acad Sci U S A 2024; 121:e2400161121. [PMID: 38478685 PMCID: PMC10963002 DOI: 10.1073/pnas.2400161121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Grain boundaries (GBs) serve not only as strong barriers to dislocation motion, but also as important carriers to accommodate plastic deformation in crystalline solids. During deformation, the inherent excess volume associated with loose atomic packing in GBs brings about a microscopic degree of freedom that can initiate GB plasticity, which is beyond the classic geometric description of GBs. However, identification of this atomistic process has long remained elusive due to its transient nature. Here, we use Au polycrystals to unveil a general and inherent route to initiating GB plasticity via a transient topological transition process triggered by the excess volume. This route underscores the general impact of a microscopic degree of freedom which is governed by a stress-triaxiality-based criterion. Our findings provide a missing perspective for developing a more comprehensive understanding of the role of GBs in plastic deformation.
Collapse
Affiliation(s)
- Qi Zhu
- Center of Electron Microscopy, State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou310027, People’s Republic of China
- School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore639798, Singapore
| | - Qingkun Zhao
- Department of Engineering Mechanics, Center for X-Mechanics, Zhejiang University, Hangzhou310027, People’s Republic of China
| | - Qishan Huang
- Department of Engineering Mechanics, Center for X-Mechanics, Zhejiang University, Hangzhou310027, People’s Republic of China
| | - Yingbin Chen
- Center of Electron Microscopy, State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou310027, People’s Republic of China
| | - Subra Suresh
- School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore639798, Singapore
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Wei Yang
- Department of Engineering Mechanics, Center for X-Mechanics, Zhejiang University, Hangzhou310027, People’s Republic of China
| | - Ze Zhang
- Center of Electron Microscopy, State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou310027, People’s Republic of China
| | - Haofei Zhou
- Department of Engineering Mechanics, Center for X-Mechanics, Zhejiang University, Hangzhou310027, People’s Republic of China
| | - Huajian Gao
- School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore639798, Singapore
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore138632, Singapore
| | - Jiangwei Wang
- Center of Electron Microscopy, State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou310027, People’s Republic of China
- Wenzhou Key Laboratory of Novel Optoelectronic and Nano Materials, Institute of Wenzhou, Zhejiang University, Wenzhou325006, People’s Republic of China
| |
Collapse
|
3
|
Zhou X, Seow WY, Ha N, Cheng TH, Jiang L, Boonruangkan J, Goh JJL, Prabhakar S, Chou N, Chen KH. Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. Nat Commun 2024; 15:2342. [PMID: 38491027 PMCID: PMC10943009 DOI: 10.1038/s41467-024-46669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
High-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs) for highly sensitive in situ profiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging ~2-35 co-expressed genes (clustered into modules) that are spatially co-localized in tissues, resulting in similar spatial information as single-gene Fluorescence In Situ Hybridization (FISH), but with ~2-20-fold higher sensitivity. Using FISHnCHIPs, we image up to 53 modules from the mouse kidney and mouse brain, and demonstrate high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPs also reveals spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables fast, robust, and scalable cell typing of tissues with normal physiology or undergoing pathogenesis.
Collapse
Affiliation(s)
- Xinrui Zhou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Wan Yi Seow
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Norbert Ha
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Teh How Cheng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Lingfan Jiang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jeeranan Boonruangkan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jolene Jie Lin Goh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Nigel Chou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
| | - Kok Hao Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
| |
Collapse
|
4
|
Do TTH, Nonahal M, Li C, Valuckas V, Tan HH, Kuznetsov AI, Nguyen HS, Aharonovich I, Ha ST. Room-temperature strong coupling in a single-photon emitter-metasurface system. Nat Commun 2024; 15:2281. [PMID: 38480721 PMCID: PMC10937668 DOI: 10.1038/s41467-024-46544-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Solid state single-photon sources with high brightness and long coherence time are promising qubit candidates for modern quantum technology. To prevent decoherence processes and preserve the integrity of the qubits, decoupling the emitters from their surrounding environment is essential. To this end, interfacing single photon emitters (SPEs) with high-finesse cavities is required, especially in the strong coupling regime, when the interaction between emitters can be mediated by cavity fields. However, achieving strong coupling at elevated temperatures is challenging due to competing incoherent processes. Here, we address this long-standing problem by using a quantum system, which comprises a class of SPEs in hexagonal boron nitride and a dielectric cavity based on bound states in the continuum (BIC). We experimentally demonstrate, at room temperature, strong coupling of the system with a large Rabi splitting of ~4 meV thanks to the combination of the narrow linewidth and large oscillator strength of the emitters and the efficient photon trapping of the BIC cavity. Our findings unveil opportunities to advance the fundamental understanding of quantum dynamical system in strong coupling regime and to realise scalable quantum devices capable of operating at room temperature.
Collapse
Affiliation(s)
- T Thu Ha Do
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), Singapore, 138634, Republic of Singapore
| | - Milad Nonahal
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- ARC Centre of Excellence for Transformative Meta-Optical Systems, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Chi Li
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- ARC Centre of Excellence for Transformative Meta-Optical Systems, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- School of Physics and Astronomy, Monash University, Melbourne, VIC, 3800, Australia
| | - Vytautas Valuckas
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), Singapore, 138634, Republic of Singapore
| | - Hark Hoe Tan
- Department of Electronic Materials Engineering, Research School of Physics and Engineering, The Australian National University, Canberra, ACT, 2600, Australia
- ARC Centre of Excellence for Transformative Meta-Optical Systems, Research School of Physics and Engineering, The Australian National University, Canberra, ACT, 2600, Australia
| | - Arseniy I Kuznetsov
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), Singapore, 138634, Republic of Singapore
| | - Hai Son Nguyen
- Univ Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Universite Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130, Ecully, France.
- Institut Universitaire de France (IUF), F-75231, Paris, France.
| | - Igor Aharonovich
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- ARC Centre of Excellence for Transformative Meta-Optical Systems, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Son Tung Ha
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), Singapore, 138634, Republic of Singapore.
| |
Collapse
|
5
|
Fang Y, Ao CK, Jiang Y, Sun Y, Chen L, Soh S. Static charge is an ionic molecular fragment. Nat Commun 2024; 15:1986. [PMID: 38443343 PMCID: PMC10914821 DOI: 10.1038/s41467-024-46200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
What is static charge? Despite the long history of research, the identity of static charge and mechanism by which static is generated by contact electrification are still unknown. Investigations are challenging due to the complexity of surfaces. This study involves the molecular-scale analysis of contact electrification using highly well-defined surfaces functionalized with a self-assembled monolayer of alkylsilanes. Analyses show the elementary molecular steps of contact electrification: the exact location of heterolytic cleavage of covalent bonds (i.e., Si-C bond), exact charged species generated (i.e., alkyl carbocation), and transfer of molecular fragments. The strong correlation between charge generation and molecular fragments due to their signature odd-even effects further shows that contact electrification is based on cleavage of covalent bonds and transfer of ionic molecular fragments. Static charge is thus an alkyl carbocation; in general, it is an ionic molecular fragment. This mechanism based on cleavage of covalent bonds is applicable to general types of insulating materials, such as covalently bonded polymers. The odd-even effect of charging caused by the difference of only one atom explains the highly sensitive nature of contact electrification.
Collapse
Affiliation(s)
- Yan Fang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30# Puzhu South Road, Nanjing, 211816, China
| | - Chi Kit Ao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Yan Jiang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Yajuan Sun
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Linfeng Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.
| |
Collapse
|
6
|
Singhal V, Chou N, Lee J, Yue Y, Liu J, Chock WK, Lin L, Chang YC, Teo EML, Aow J, Lee HK, Chen KH, Prabhakar S. BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nat Genet 2024; 56:431-441. [PMID: 38413725 PMCID: PMC10937399 DOI: 10.1038/s41588-024-01664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY's spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can also be used for quality control of spatial transcriptomics data and for spatially aware batch effect correction. Importantly, it is substantially faster and more scalable than existing methods, enabling the processing of millions of cell datasets. In summary, BANKSY provides an accurate, biologically motivated, scalable and versatile framework for analyzing spatially resolved omics data.
Collapse
Affiliation(s)
- Vipul Singhal
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Nigel Chou
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joseph Lee
- Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Yifei Yue
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Republic of Singapore
| | - Jinyue Liu
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Wan Kee Chock
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Li Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | | | | | - Jonathan Aow
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Hwee Kuan Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- School of Computing, National University of Singapore, Singapore, Republic of Singapore
- Singapore Eye Research Institute, Singapore, Republic of Singapore
- International Research Laboratory on Artificial Intelligence, Singapore, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Kok Hao Chen
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
| | - Shyam Prabhakar
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore.
| |
Collapse
|
7
|
Yang Q, Han D, Zhao S, Kang J, Wang F, Lee SC, Lei J, Lee KJ, Park BG, Yang H. Field-free spin-orbit torque switching in ferromagnetic trilayers at sub-ns timescales. Nat Commun 2024; 15:1814. [PMID: 38418454 PMCID: PMC10901790 DOI: 10.1038/s41467-024-46113-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
Current-induced spin torques enable the electrical control of the magnetization with low energy consumption. Conventional magnetic random access memory (MRAM) devices rely on spin-transfer torque (STT), this however limits MRAM applications because of the nanoseconds incubation delay and associated endurance issues. A potential alternative to STT is spin-orbit torque (SOT). However, for practical, high-speed SOT devices, it must satisfy three conditions simultaneously, i.e., field-free switching at short current pulses, short incubation delay, and low switching current. Here, we demonstrate field-free SOT switching at sub-ns timescales in a CoFeB/Ti/CoFeB ferromagnetic trilayer, which satisfies all three conditions. In this trilayer, the bottom magnetic layer or its interface generates spin currents with polarizations in both in-plane and out-of-plane components. The in-plane component reduces the incubation time, while the out-of-plane component realizes field-free switching at a low current. Our results offer a field-free SOT solution for energy-efficient scalable MRAM applications.
Collapse
Affiliation(s)
- Qu Yang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Donghyeon Han
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Shishun Zhao
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Jaimin Kang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Fei Wang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Sung-Chul Lee
- Next Generation Process Development Team, Semiconductor R&D Center, Samsung Electronics Co. Ltd., Hwaseong, Gyeonggi, 18448, Korea
| | - Jiayu Lei
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Kyung-Jin Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Byong-Guk Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Hyunsoo Yang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117576, Singapore.
| |
Collapse
|
8
|
Ayyangar U, Karkhanis A, Tay H, Afandi AFB, Bhattacharjee O, Ks L, Lee SH, Chan J, Raghavan S. Metabolic rewiring of macrophages by epidermal-derived lactate promotes sterile inflammation in the murine skin. EMBO J 2024:10.1038/s44318-024-00039-y. [PMID: 38418556 DOI: 10.1038/s44318-024-00039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 03/01/2024] Open
Abstract
Dysregulated macrophage responses and changes in tissue metabolism are hallmarks of chronic inflammation in the skin. However, the metabolic cues that direct and support macrophage functions in the skin are poorly understood. Here, we show that during sterile skin inflammation, the epidermis and macrophages uniquely depend on glycolysis and the TCA cycle, respectively. This compartmentalisation is initiated by ROS-induced HIF-1α stabilization leading to enhanced glycolysis in the epidermis. The end-product of glycolysis, lactate, is then exported by epithelial cells and utilized by the dermal macrophages to induce their M2-like fates through NF-κB pathway activation. In addition, we show that psoriatic skin disorder is also driven by such lactate metabolite-mediated crosstalk between the epidermis and macrophages. Notably, small-molecule inhibitors of lactate transport in this setting attenuate sterile inflammation and psoriasis disease burden, and suppress M2-like fate acquisition in dermal macrophages. Our study identifies an essential role for the metabolite lactate in regulating macrophage responses to inflammation, which may be effectively targeted to treat inflammatory skin disorders such as psoriasis.
Collapse
Affiliation(s)
- Uttkarsh Ayyangar
- Centre for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.
- School for Chemical and Biotechnology, Sastra University, Thanjavur, India.
| | - Aneesh Karkhanis
- A*Star Skin Research Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Heather Tay
- A*Star Skin Research Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Oindrila Bhattacharjee
- Centre for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Lalitha Ks
- Animal Care and Resource Centre (ACRC), National Centre for Biological Sciences (NCBS), Bangalore, India
| | - Sze Han Lee
- A*Star Skin Research Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - James Chan
- A*Star Skin Research Labs, Agency for Science, Technology and Research, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science Technology and Research, Singapore, Singapore
| | - Srikala Raghavan
- Centre for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.
- A*Star Skin Research Labs, Agency for Science, Technology and Research, Singapore, Singapore.
| |
Collapse
|
9
|
Wang B, Wang M, Fan Z, Ma C, Xi S, Chang LY, Zhang M, Ling N, Mi Z, Chen S, Leow WR, Zhang J, Wang D, Lum Y. Nanocurvature-induced field effects enable control over the activity of single-atom electrocatalysts. Nat Commun 2024; 15:1719. [PMID: 38409205 PMCID: PMC10897157 DOI: 10.1038/s41467-024-46175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Tuning interfacial electric fields provides a powerful means to control electrocatalyst activity. Importantly, electric fields can modify adsorbate binding energies based on their polarizability and dipole moment, and hence operate independently of scaling relations that fundamentally limit performance. However, implementation of such a strategy remains challenging because typical methods modify the electric field non-uniformly and affects only a minority of active sites. Here we discover that uniformly tunable electric field modulation can be achieved using a model system of single-atom catalysts (SACs). These consist of M-N4 active sites hosted on a series of spherical carbon supports with varying degrees of nanocurvature. Using in-situ Raman spectroscopy with a Stark shift reporter, we demonstrate that a larger nanocurvature induces a stronger electric field. We show that this strategy is effective over a broad range of SAC systems and electrocatalytic reactions. For instance, Ni SACs with optimized nanocurvature achieved a high CO partial current density of ~400 mA cm-2 at >99% Faradaic efficiency for CO2 reduction in acidic media.
Collapse
Affiliation(s)
- Bingqing Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Meng Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Ziting Fan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Chao Ma
- Department of Chemistry, Tsinghua University, Tsinghua, China
| | - Shibo Xi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Lo-Yueh Chang
- National Synchrotron Radiation Research Centre, Hsinchu, Taiwan
| | - Mingsheng Zhang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Ning Ling
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Ziyu Mi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Shenghua Chen
- Department of Chemistry, Tsinghua University, Tsinghua, China
| | - Wan Ru Leow
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Jia Zhang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology, and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Dingsheng Wang
- Department of Chemistry, Tsinghua University, Tsinghua, China
| | - Yanwei Lum
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore.
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore.
| |
Collapse
|
10
|
Bae KH, Shunmuganathan B, Zhang L, Lim A, Gupta R, Wang Y, Chua BL, Wang Y, Gu Y, Qian X, Tan ISL, Purushotorman K, MacAry PA, White KP, Yang YY. Durable cross-protective neutralizing antibody responses elicited by lipid nanoparticle-formulated SARS-CoV-2 mRNA vaccines. NPJ Vaccines 2024; 9:43. [PMID: 38396073 PMCID: PMC10891077 DOI: 10.1038/s41541-024-00835-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The advent of SARS-CoV-2 variants with defined mutations that augment pathogenicity and/or increase immune evasiveness continues to stimulate global efforts to improve vaccine formulation and efficacy. The extraordinary advantages of lipid nanoparticles (LNPs), including versatile design, scalability, and reproducibility, make them ideal candidates for developing next-generation mRNA vaccines against circulating SARS-CoV-2 variants. Here, we assess the efficacy of LNP-encapsulated mRNA booster vaccines encoding the spike protein of SARS-CoV-2 for variants of concern (Delta, Omicron) and using a predecessor (YN2016C isolated from bats) strain spike protein to elicit durable cross-protective neutralizing antibody responses. The mRNA-LNP vaccines have desirable physicochemical characteristics, such as small size (~78 nm), low polydispersity index (<0.13), and high encapsulation efficiency (>90%). We employ in vivo bioluminescence imaging to illustrate the capacity of our LNPs to induce robust mRNA expression in secondary lymphoid organs. In a BALB/c mouse model, a three-dose subcutaneous immunization of mRNA-LNPs vaccines achieved remarkably high levels of cross-neutralization against the Omicron B1.1.529 and BA.2 variants for extended periods of time (28 weeks) with good safety profiles for all constructs when used in a booster regime, including the YN2016C bat virus sequences. These findings have important implications for the design of mRNA-LNP vaccines that aim to trigger durable cross-protective immunity against the current and newly emerging variants.
Collapse
Affiliation(s)
- Ki Hyun Bae
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Bhuvaneshwari Shunmuganathan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Li Zhang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Andrew Lim
- Provaxus, Inc, Dover, Delaware, 19901, USA
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Yanming Wang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Boon Lin Chua
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Yang Wang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Republic of Singapore
| | - Yue Gu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Xinlei Qian
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Isabelle Siang Ling Tan
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Kiren Purushotorman
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Paul A MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore.
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore.
| | - Kevin P White
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Republic of Singapore.
- Department of Biochemistry and Precision Medicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Republic of Singapore.
| | - Yi Yan Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore.
| |
Collapse
|
11
|
Jani H, Harrison J, Hooda S, Prakash S, Nandi P, Hu J, Zeng Z, Lin JC, Godfrey C, Omar GJ, Butcher TA, Raabe J, Finizio S, Thean AVY, Ariando A, Radaelli PG. Spatially reconfigurable antiferromagnetic states in topologically rich free-standing nanomembranes. Nat Mater 2024:10.1038/s41563-024-01806-2. [PMID: 38374414 DOI: 10.1038/s41563-024-01806-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 01/11/2024] [Indexed: 02/21/2024]
Abstract
Antiferromagnets hosting real-space topological textures are promising platforms to model fundamental ultrafast phenomena and explore spintronics. However, they have only been epitaxially fabricated on specific symmetry-matched substrates, thereby preserving their intrinsic magneto-crystalline order. This curtails their integration with dissimilar supports, restricting the scope of fundamental and applied investigations. Here we circumvent this limitation by designing detachable crystalline antiferromagnetic nanomembranes of α-Fe2O3. First, we show-via transmission-based antiferromagnetic vector mapping-that flat nanomembranes host a spin-reorientation transition and rich topological phenomenology. Second, we exploit their extreme flexibility to demonstrate the reconfiguration of antiferromagnetic states across three-dimensional membrane folds resulting from flexure-induced strains. Finally, we combine these developments using a controlled manipulator to realize the strain-driven non-thermal generation of topological textures at room temperature. The integration of such free-standing antiferromagnetic layers with flat/curved nanostructures could enable spin texture designs via magnetoelastic/geometric effects in the quasi-static and dynamical regimes, opening new explorations into curvilinear antiferromagnetism and unconventional computing.
Collapse
Affiliation(s)
- Hariom Jani
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
- Department of Physics, National University of Singapore, Singapore, Singapore.
| | - Jack Harrison
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Sonu Hooda
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
| | - Saurav Prakash
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Proloy Nandi
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Junxiong Hu
- Department of Physics, National University of Singapore, Singapore, Singapore.
| | - Zhiyang Zeng
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Jheng-Cyuan Lin
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Charles Godfrey
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Ganesh Ji Omar
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Tim A Butcher
- Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland
| | - Jörg Raabe
- Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland
| | - Simone Finizio
- Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland.
| | - Aaron Voon-Yew Thean
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, Singapore
| | - A Ariando
- Department of Physics, National University of Singapore, Singapore, Singapore.
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, Singapore.
| | - Paolo G Radaelli
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| |
Collapse
|
12
|
Song S, Pinar Solé A, Matěj A, Li G, Stetsovych O, Soler D, Yang H, Telychko M, Li J, Kumar M, Chen Q, Edalatmanesh S, Brabec J, Veis L, Wu J, Jelinek P, Lu J. Highly entangled polyradical nanographene with coexisting strong correlation and topological frustration. Nat Chem 2024:10.1038/s41557-024-01453-9. [PMID: 38374456 DOI: 10.1038/s41557-024-01453-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/17/2024] [Indexed: 02/21/2024]
Abstract
Open-shell nanographenes exhibit unconventional π-magnetism arising from topological frustration or strong electron-electron interaction. However, conventional design approaches are typically limited to a single magnetic origin, which can restrict the number of correlated spins or the type of magnetic ordering in open-shell nanographenes. Here we present a design strategy that combines topological frustration and electron-electron interactions to fabricate a large fully fused 'butterfly'-shaped tetraradical nanographene on Au(111). We employ bond-resolved scanning tunnelling microscopy and spin-excitation spectroscopy to resolve the molecular backbone and reveal the strongly correlated open-shell character, respectively. This nanographene contains four unpaired electrons with both ferromagnetic and anti-ferromagnetic interactions, harbouring a many-body singlet ground state and strong multi-spin entanglement, which is well described by many-body calculations. Furthermore, we study the magnetic properties and spin states in the nanographene using a nickelocene magnetic probe. The ability to imprint and characterize many-body strongly correlated spins in polyradical nanographenes paves the way for future advancements in quantum information technologies.
Collapse
Affiliation(s)
- Shaotang Song
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Andrés Pinar Solé
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Adam Matěj
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Guangwu Li
- Department of Chemistry, National University of Singapore, Singapore, Singapore
- Center of Single-Molecule Sciences, Frontiers Science Center for New Organic Matter, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | | | - Diego Soler
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Huimin Yang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Mykola Telychko
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Jing Li
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Manish Kumar
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Qifan Chen
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Jiri Brabec
- Department of Theoretical Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Libor Veis
- Department of Theoretical Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic.
| | - Jishan Wu
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
| | - Pavel Jelinek
- Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Jiong Lu
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore.
- National University of Singapore (Suzhou) Research Institute, Suzhou, China.
| |
Collapse
|
13
|
Wu Y, Teh YC, Chong SZ. Going Full TeRM: The Seminal Role of Tissue-Resident Macrophages in Organ Remodeling during Pregnancy and Lactation. J Immunol 2024; 212:513-521. [PMID: 38315948 DOI: 10.4049/jimmunol.2300560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/23/2023] [Indexed: 02/07/2024]
Abstract
During pregnancy and lactation, the uterus and mammary glands undergo remarkable structural changes to perform their critical reproductive functions before reverting to their original dormant state upon childbirth and weaning, respectively. Underlying this incredible plasticity are complex remodeling processes that rely on coordinated decisions at both the cellular and tissue-subunit levels. With their exceptional versatility, tissue-resident macrophages play a variety of supporting roles in these organs during each stage of development, ranging from maintaining immune homeostasis to facilitating tissue remodeling, although much remains to be discovered about the identity and regulation of individual macrophage subsets. In this study, we review the increasingly appreciated contributions of these immune cells to the reproductive process and speculate on future lines of inquiry. Deepening our understanding of their interactions with the parenchymal or stromal populations in their respective niches may reveal new strategies to ameliorate complications in pregnancy and breastfeeding, thereby improving maternal health and well-being.
Collapse
Affiliation(s)
- Yixuan Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Ye Chean Teh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| |
Collapse
|
14
|
Wang M, Wang B, Zhang J, Xi S, Ling N, Mi Z, Yang Q, Zhang M, Leow WR, Zhang J, Lum Y. Acidic media enables oxygen-tolerant electrosynthesis of multicarbon products from simulated flue gas. Nat Commun 2024; 15:1218. [PMID: 38336956 PMCID: PMC10858036 DOI: 10.1038/s41467-024-45527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Renewable electricity powered electrochemical CO2 reduction (CO2R) offers a valuable method to close the carbon cycle and reduce our overreliance on fossil fuels. However, high purity CO2 is usually required as feedstock, which potentially decreases the feasibility and economic viability of the process. Direct conversion of flue gas is an attractive option but is challenging due to the low CO2 concentration and the presence of O2 impurities. As a result, up to 99% of the applied current can be lost towards the undesired oxygen reduction reaction (ORR). Here, we show that acidic electrolyte can significantly suppress ORR on Cu, enabling generation of multicarbon products from simulated flue gas. Using a composite Cu and carbon supported single-atom Ni tandem electrocatalyst, we achieved a multicarbon Faradaic efficiency of 46.5% at 200 mA cm-2, which is ~20 times higher than bare Cu under alkaline conditions. We also demonstrate stable performance for 24 h with a multicarbon product full-cell energy efficiency of 14.6%. Strikingly, this result is comparable to previously reported acidic CO2R systems using pure CO2. Our findings demonstrate a potential pathway towards designing efficient electrolyzers for direct conversion of flue gas to value-added chemicals and fuels.
Collapse
Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Bingqing Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore.
| | - Jiguang Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Shibo Xi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Ning Ling
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Ziyu Mi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Qin Yang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore
| | - Mingsheng Zhang
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Wan Ru Leow
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Singapore, 627833, Republic of Singapore
| | - Jia Zhang
- Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Yanwei Lum
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Republic of Singapore.
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore.
| |
Collapse
|
15
|
Wu Q, Dai C, Meng F, Jiao Y, Xu ZJ. Potential and electric double-layer effect in electrocatalytic urea synthesis. Nat Commun 2024; 15:1095. [PMID: 38321031 PMCID: PMC10847171 DOI: 10.1038/s41467-024-45522-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Electrochemical synthesis is a promising way for sustainable urea production, yet the exact mechanism has not been fully revealed. Herein, we explore the mechanism of electrochemical coupling of nitrite and carbon dioxide on Cu surfaces towards urea synthesis on the basis of a constant-potential method combined with an implicit solvent model. The working electrode potential, which has normally overlooked, is found influential on both the reaction mechanism and activity. The further computational study on the reaction pathways reveals that *CO-NH and *NH-CO-NH as the key intermediates. In addition, through the analysis of turnover frequencies under various potentials, pressures, and temperatures within a microkinetic model, we demonstrate that the activity increases with temperature, and the Cu(100) shows the highest efficiency towards urea synthesis among all three Cu surfaces. The electric double-layer capacitance also plays a key role in urea synthesis. Based on these findings, we propose two essential strategies to promote the efficiency of urea synthesis on Cu electrodes: increasing Cu(100) surface ratio and elevating the reaction temperature.
Collapse
Affiliation(s)
- Qian Wu
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chencheng Dai
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- The Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE way, Singapore, 138602, Singapore
| | - Fanxu Meng
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yan Jiao
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Zhichuan J Xu
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
- The Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE way, Singapore, 138602, Singapore.
- Energy Research Institute @ Nanyang Technological University, ERI@N, Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
- Center for Advanced Catalysis Science and Technology, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| |
Collapse
|
16
|
Pranantyo D, Yeo CK, Wu Y, Fan C, Xu X, Yip YS, Vos MIG, Mahadevegowda SH, Lim PLK, Yang L, Hammond PT, Leavesley DI, Tan NS, Chan-Park MB. Hydrogel dressings with intrinsic antibiofilm and antioxidative dual functionalities accelerate infected diabetic wound healing. Nat Commun 2024; 15:954. [PMID: 38296937 PMCID: PMC10830466 DOI: 10.1038/s41467-024-44968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Chronic wounds are often infected with biofilm bacteria and characterized by high oxidative stress. Current dressings that promote chronic wound healing either require additional processes such as photothermal irradiation or leave behind gross amounts of undesirable residues. We report a dual-functionality hydrogel dressing with intrinsic antibiofilm and antioxidative properties that are synergistic and low-leaching. The hydrogel is a crosslinked network with tethered antibacterial cationic polyimidazolium and antioxidative N-acetylcysteine. In a murine diabetic wound model, the hydrogel accelerates the closure of wounds infected with methicillin-resistant Staphylococcus aureus or carbapenem-resistant Pseudomonas aeruginosa biofilm. Furthermore, a three-dimensional ex vivo human skin equivalent model shows that N-acetylcysteine promotes the keratinocyte differentiation and accelerates the re-epithelialization process. Our hydrogel dressing can be made into different formats for the healing of both flat and deep infected chronic wounds without contamination of the wound or needing other modalities such as photothermal irradiation.
Collapse
Affiliation(s)
- Dicky Pranantyo
- Centre for Antimicrobial Bioengineering, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Chun Kiat Yeo
- Centre for Antimicrobial Bioengineering, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
- NTU Institute for Health Technologies, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, 637553, Singapore
| | - Yang Wu
- Centre for Antimicrobial Bioengineering, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Chen Fan
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 11 Mandalay Road, Singapore, 308232, Singapore
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Xiaofei Xu
- Centre for Antimicrobial Bioengineering, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Yun Sheng Yip
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Marcus Ivan Gerard Vos
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Surendra H Mahadevegowda
- Centre for Antimicrobial Bioengineering, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Priscilla Lay Keng Lim
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 11 Mandalay Road, Singapore, 308232, Singapore
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Paula T Hammond
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - David Ian Leavesley
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 11 Mandalay Road, Singapore, 308232, Singapore
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Mary B Chan-Park
- Centre for Antimicrobial Bioengineering, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
17
|
Lin QXX, Rajagopalan D, Gamage AM, Tan LM, Venkatesh PN, Chan WOY, Kumar D, Agrawal R, Chen Y, Fong SW, Singh A, Sun LJ, Tan SY, Chai LYA, Somani J, Lee B, Renia L, Ng LFP, Ramanathan K, Wang LF, Young B, Lye D, Singhal A, Prabhakar S. Longitudinal single cell atlas identifies complex temporal relationship between type I interferon response and COVID-19 severity. Nat Commun 2024; 15:567. [PMID: 38238298 PMCID: PMC10796319 DOI: 10.1038/s41467-023-44524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
Due to the paucity of longitudinal molecular studies of COVID-19, particularly those covering the early stages of infection (Days 1-8 symptom onset), our understanding of host response over the disease course is limited. We perform longitudinal single cell RNA-seq on 286 blood samples from 108 age- and sex-matched COVID-19 patients, including 73 with early samples. We examine discrete cell subtypes and continuous cell states longitudinally, and we identify upregulation of type I IFN-stimulated genes (ISGs) as the predominant early signature of subsequent worsening of symptoms, which we validate in an independent cohort and corroborate by plasma markers. However, ISG expression is dynamic in progressors, spiking early and then rapidly receding to the level of severity-matched non-progressors. In contrast, cross-sectional analysis shows that ISG expression is deficient and IFN suppressors such as SOCS3 are upregulated in severe and critical COVID-19. We validate the latter in four independent cohorts, and SOCS3 inhibition reduces SARS-CoV-2 replication in vitro. In summary, we identify complexity in type I IFN response to COVID-19, as well as a potential avenue for host-directed therapy.
Collapse
Affiliation(s)
- Quy Xiao Xuan Lin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Deepa Rajagopalan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Le Min Tan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Prasanna Nori Venkatesh
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Dilip Kumar
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Yao Chen
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Louisa J Sun
- Alexandra Hospital, Singapore, 159964, Singapore
| | - Seow-Yen Tan
- Changi General Hospital, Singapore, 529889, Singapore
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Kollengode Ramanathan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- National University Hospital, Singapore, 119074, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, 168753, Singapore
| | - Barnaby Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - David Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Amit Singhal
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore.
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore.
| | - Shyam Prabhakar
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore.
| |
Collapse
|
18
|
Wang F, Zhu S, Chen W, Han J, Duan R, Wang C, Dai M, Sun F, Jin Y, Wang QJ. Multidimensional detection enabled by twisted black arsenic-phosphorus homojunctions. Nat Nanotechnol 2024:10.1038/s41565-023-01593-y. [PMID: 38225358 DOI: 10.1038/s41565-023-01593-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
A light field carrying multidimensional optical information, including but not limited to polarization, intensity and wavelength, is essential for numerous applications such as environmental monitoring, thermal imaging, medical diagnosis and free-space communications. Simultaneous acquisition of this multidimensional information could provide comprehensive insights for understanding complex environments but remains a challenge. Here we demonstrate a multidimensional optical information detection device based on zero-bias double twisted black arsenic-phosphorus homojunctions, where the photoresponse is dominated by the photothermoelectric effect. By using a bipolar and phase-offset polarization photoresponse, the device operated in the mid-infrared range can simultaneously detect both the polarization angle and incident intensity information through direct measurement of the photocurrents in the double twisted black arsenic-phosphorus homojunctions. The device's responsivity makes it possible to retrieve wavelength information, typically perceived as difficult to obtain. Moreover, the device exhibits an electrically tunable polarization photoresponse, enabling precise distinction of polarization angles under low-intensity light exposure. These demonstrations offer a promising approach for simultaneous detection of multidimensional optical information, indicating potential for diverse photonic applications.
Collapse
Affiliation(s)
- Fakun Wang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Song Zhu
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Wenduo Chen
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jiayue Han
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ruihuan Duan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Chongwu Wang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mingjin Dai
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Fangyuan Sun
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yuhao Jin
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qi Jie Wang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore.
- Centre for Disruptive Photonic Technologies, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
19
|
Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024; 15:389. [PMID: 38195598 PMCID: PMC10776679 DOI: 10.1038/s41467-023-44555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
Collapse
Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Philip R Baldwin
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shi Min Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- College of Pharmacy, Kyung Hee University, Seoul, 02247, Republic of Korea
| | - Atousa Mehrani
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gordon Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Benjamin A Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Joseph A P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
20
|
Tay DWP, Tan LL, Heng E, Zulkarnain N, Ching KC, Wibowo M, Chin EJ, Tan ZYQ, Leong CY, Ng VWP, Yang LK, Seow DCS, Lim YW, Koh W, Koduru L, Kanagasundaram Y, Ng SB, Lim YH, Wong FT. Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes. Commun Biol 2024; 7:50. [PMID: 38184720 PMCID: PMC10771470 DOI: 10.1038/s42003-023-05648-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Natural products possess significant therapeutic potential but remain underutilized despite advances in genomics and bioinformatics. While there are approaches to activate and upregulate natural product biosynthesis in both native and heterologous microbial strains, a comprehensive strategy to elicit production of natural products as well as a generalizable and efficient method to interrogate diverse native strains collection, remains lacking. Here, we explore a flexible and robust integrase-mediated multi-pronged activation approach to reliably perturb and globally trigger antibiotics production in actinobacteria. Across 54 actinobacterial strains, our approach yielded 124 distinct activator-strain combinations which consistently outperform wild type. Our approach expands accessible metabolite space by nearly two-fold and increases selected metabolite yields by up to >200-fold, enabling discovery of Gram-negative bioactivity in tetramic acid analogs. We envision these findings as a gateway towards a more streamlined, accelerated, and scalable strategy to unlock the full potential of Nature's chemical repertoire.
Collapse
Grants
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917003 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- National Research Foundation Singapore (National Research Foundation-Prime Minister’s office, Republic of Singapore)
Collapse
Affiliation(s)
- Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Lee Ling Tan
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Nadiah Zulkarnain
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Elaine Jinfeng Chin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Zann Yi Qi Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Veronica Wee Pin Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Deborah C S Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yi Wee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Winston Koh
- Bioinformatics Institute (BII), Agency of Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Republic of Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore.
| | - Fong Tian Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore.
| |
Collapse
|
21
|
Peh G, Tay T, Tan LL, Tiong E, Bi J, Goh YL, Ye S, Lin F, Tan CJX, Tan YZ, Wong J, Zhao H, Wong FT, Ang EL, Lim YH. Site-selective chlorination of pyrrolic heterocycles by flavin dependent enzyme PrnC. Commun Chem 2024; 7:7. [PMID: 38182798 PMCID: PMC10770391 DOI: 10.1038/s42004-023-01083-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Halogenation of pyrrole requires strong electrophilic reagents and often leads to undesired polyhalogenated products. Biocatalytic halogenation is a highly attractive approach given its chemoselectivity and benign reaction conditions. While there are several reports of enzymatic phenol and indole halogenation in organic synthesis, corresponding reports on enzymatic pyrrole halogenation have been lacking. Here we describe the in vitro functional and structural characterization of PrnC, a flavin-dependent halogenase that can act on free-standing pyrroles. Computational modeling and site mutagenesis studies identified three key residues in the catalytic pocket. A moderate resolution map using single-particle cryogenic electron microscopy reveals PrnC to be a dimer. This native PrnC can halogenate a library of structurally diverse pyrrolic heterocycles in a site-selective manner and be applied in the chemoenzymatic synthesis of a chlorinated analog of the agrochemical fungicide Fludioxonil.
Collapse
Affiliation(s)
- GuangRong Peh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Terence Tay
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Lee Ling Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Elaine Tiong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Jiawu Bi
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Yi Ling Goh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Suming Ye
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Fu Lin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Cheryl Jia Xin Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yong Zi Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joel Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fong Tian Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
| |
Collapse
|
22
|
Sun S, Dai C, Zhao P, Xi S, Ren Y, Tan HR, Lim PC, Lin M, Diao C, Zhang D, Wu C, Yu A, Koh JCJ, Lieu WY, Seng DHL, Sun L, Li Y, Tan TL, Zhang J, Xu ZJ, Seh ZW. Spin-related Cu-Co pair to increase electrochemical ammonia generation on high-entropy oxides. Nat Commun 2024; 15:260. [PMID: 38177119 PMCID: PMC10766993 DOI: 10.1038/s41467-023-44587-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
The electrochemical conversion of nitrate to ammonia is a way to eliminate nitrate pollutant in water. Cu-Co synergistic effect was found to produce excellent performance in ammonia generation. However, few studies have focused on this effect in high-entropy oxides. Here, we report the spin-related Cu-Co synergistic effect on electrochemical nitrate-to-ammonia conversion using high-entropy oxide Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O. In contrast, the Li-incorporated MgCoNiCuZnO exhibits inferior performance. By correlating the electronic structure, we found that the Co spin states are crucial for the Cu-Co synergistic effect for ammonia generation. The Cu-Co pair with a high spin Co in Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O can facilitate ammonia generation, while a low spin Co in Li-incorporated MgCoNiCuZnO decreases the Cu-Co synergistic effect on ammonia generation. These findings offer important insights in employing the synergistic effect and spin states inside for selective catalysis. It also indicates the generality of the magnetic effect in ammonia synthesis between electrocatalysis and thermal catalysis.
Collapse
Affiliation(s)
- Shengnan Sun
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Chencheng Dai
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Republic of Singapore
- The Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, Singapore, 138602, Republic of Singapore
| | - Peng Zhao
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Shibo Xi
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE²), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore, 627833, Republic of Singapore
| | - Yi Ren
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Hui Ru Tan
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Poh Chong Lim
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Ming Lin
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Caozheng Diao
- Singapore Synchrotron Light Sources (SSLS), National University of Singapore, 5 Research Link, Singapore, 117603, Republic of Singapore
| | - Danwei Zhang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Chao Wu
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE²), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore, 627833, Republic of Singapore
- College of Materials Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Anke Yu
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Republic of Singapore
| | - Jie Cheng Jackson Koh
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Republic of Singapore
| | - Wei Ying Lieu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Republic of Singapore
| | - Debbie Hwee Leng Seng
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Libo Sun
- The Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, Singapore, 138602, Republic of Singapore
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, P. R. China
| | - Yuke Li
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Teck Leong Tan
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Jia Zhang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore.
| | - Zhichuan J Xu
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Republic of Singapore.
| | - Zhi Wei Seh
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore.
| |
Collapse
|
23
|
Zheng XT, Goh WP, Yu Y, Sutarlie L, Chen DY, Tan SCL, Jiang C, Zhao M, Ba T, Li H, Su X, Yang L. Skin-Attachable Ink-Dispenser-Printed Paper Fluidic Sensor Patch for Colorimetric Sweat Analysis. Adv Healthc Mater 2024; 13:e2302173. [PMID: 37897264 DOI: 10.1002/adhm.202302173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/09/2023] [Indexed: 10/30/2023]
Abstract
In situ analysis of sweat biomarkers potentially provides noninvasive lifestyle monitoring and early diagnosis. Quantitative detection of sweat rate is crucial for thermoregulation and preventing heat injuries. Here, a skin-attachable paper fluidic patch is reported for in situ colorimetric sensing of multiple sweat markers (pH, glucose, lactate, and uric acid) with concurrent sweat rate tracking. Two sets of fluidic patterns-multiplexed detection zones and a longitudinal sweat rate channel-are directly printed by an automated ink dispenser from a specially developed ceramic-based ink. The ceramic ink thermal-cures into an impervious barrier, confining sweat within the channels. The ceramic-ink-printed boundary achieves higher pattern resolution, prevents fluid leakage, attains pattern thermal stability, and resistant to organic solvents. The cellulose matrix of the detection zones is modified with nanoparticles to improve the color homogeneity and sweat sensor sensitivity. The sweat rate channel is made moisture sensitive by incorporating a metal-salt-based dye. The change in saturation/color of the detection zones and/or channels upon sweat addition can be visually detected or quantified by a smartphone camera. A cost-effective way is provided to fabricate paper fluidic sensor patches, successfully demonstrating on-body multiplexed evaluation of sweat analytes. Such skin wearables offer on-site analysis, meaningful to an increasingly health-conscious population.
Collapse
Affiliation(s)
- Xin Ting Zheng
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Wei Peng Goh
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Yong Yu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Laura Sutarlie
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Der Ying Chen
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Republic of Singapore
| | - Sherwin Chong Li Tan
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Changyun Jiang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Meng Zhao
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Te Ba
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, Connexis #16-16, Singapore, 138632, Republic of Singapore
| | - Hongying Li
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, Connexis #16-16, Singapore, 138632, Republic of Singapore
| | - Xiaodi Su
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Republic of Singapore
| | - Le Yang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore, 117575, Republic of Singapore
| |
Collapse
|
24
|
Teh BS, Hii YS, Hinks J, Abdul-Wahab MF, Swarup S. Complete genome sequence of Methylomonas sp. UP202 isolated from an urban waterway sediment. Microbiol Resour Announc 2023; 12:e0063323. [PMID: 37982654 PMCID: PMC10720544 DOI: 10.1128/mra.00633-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/14/2023] [Indexed: 11/21/2023] Open
Abstract
We report the complete genome sequence of Methylomonas sp. UP202 isolated from an urban waterway sediment in Singapore. The genome contains genes involved in methane, methanol, formaldehyde, and formate oxidation. It also contains genes utilizing various nitrogen sources such as nitrogen, nitrate, nitrite, urea, and ammonium.
Collapse
Affiliation(s)
- Beng-Soon Teh
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Yiik-Siang Hii
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mohd Firdaus Abdul-Wahab
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| |
Collapse
|
25
|
Teo HC, Tan NHL, Zheng Q, Lim AJY, Sreekar R, Chen X, Zhou Y, Sarira TV, De Alban JDT, Tang H, Friess DA, Koh LP. Uncertainties in deforestation emission baseline methodologies and implications for carbon markets. Nat Commun 2023; 14:8277. [PMID: 38092814 PMCID: PMC10719246 DOI: 10.1038/s41467-023-44127-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Carbon credits generated through jurisdictional-scale avoided deforestation projects require accurate estimates of deforestation emission baselines, but there are serious challenges to their robustness. We assessed the variability, accuracy, and uncertainty of baselining methods by applying sensitivity and variable importance analysis on a range of typically-used methods and parameters for 2,794 jurisdictions worldwide. The median jurisdiction's deforestation emission baseline varied by 171% (90% range: 87%-440%) of its mean, with a median forecast error of 0.778 times (90% range: 0.548-3.56) the actual deforestation rate. Moreover, variable importance analysis emphasised the strong influence of the deforestation projection approach. For the median jurisdiction, 68.0% of possible methods (90% range: 61.1%-85.6%) exceeded 15% uncertainty. Tropical and polar biomes exhibited larger uncertainties in carbon estimations. The use of sensitivity analyses, multi-model, and multi-source ensemble approaches could reduce variabilities and biases. These findings provide a roadmap for improving baseline estimations to enhance carbon market integrity and trust.
Collapse
Affiliation(s)
- Hoong Chen Teo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore.
| | - Nicole Hui Li Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
| | - Qiming Zheng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
- Department of Land Surveying and Geo-Informatics, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Annabel Jia Yi Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
| | - Rachakonda Sreekar
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | - Xiao Chen
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Yuchuan Zhou
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Tasya Vadya Sarira
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Jose Don T De Alban
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
| | - Hao Tang
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Daniel A Friess
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
- Department of Earth and Environmental Sciences, Tulane University, New Orleans, LA, USA
| | - Lian Pin Koh
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore.
- Department of Geography, National University of Singapore, Singapore, Singapore.
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
26
|
Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
Collapse
Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| |
Collapse
|
27
|
Lê-Bury G, Chen Y, Rhen JM, Grenier JK, Singhal A, Russell DG, Boliar S. HIV-1 active and latent infections induce disparate chromatin reorganization and transcriptional regulation of mRNAs and lncRNAs in SupT1 cells. mBio 2023; 14:e0261923. [PMID: 38038477 PMCID: PMC10746154 DOI: 10.1128/mbio.02619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE HIV-1 infection of T-lymphocytes depends on co-opting cellular transcriptional and translational machineries for viral replication. This requires significant changes in the cellular microenvironment. We have characterized and compared the changes in cellular chromatin structures as well as gene expression landscapes in T cells that are either actively or latently infected with HIV-1. Our results reveal that chromatin accessibility and expression of both protein-coding mRNAs and non-coding lncRNAs are uniquely regulated in HIV-1-infected T cells, depending on whether the virus is actively transcribing or remains in a transcriptionally silent, latent state. HIV-1 latent infection elicits more robust changes in the cellular chromatin organization than active viral infection. Our analysis also identifies the effects of such epigenomic changes on the cellular gene expression and subsequent biological pathways. This study comprehensively characterizes the cellular epigenomic and transcriptomic states that support active and latent HIV-1 infection in an in vitro model of SupT1 cells.
Collapse
Affiliation(s)
- Gabrielle Lê-Bury
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yao Chen
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jordan M. Rhen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcription Regulation and Expression Facility, Cornell University, Ithaca, New York, USA
| | - Amit Singhal
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore, Singapore
| | - David G. Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Saikat Boliar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| |
Collapse
|
28
|
Fang H, Mahalingam H, Li X, Han X, Qiu Z, Han Y, Noori K, Dulal D, Chen H, Lyu P, Yang T, Li J, Su C, Chen W, Cai Y, Neto AHC, Novoselov KS, Rodin A, Lu J. Atomically precise vacancy-assembled quantum antidots. Nat Nanotechnol 2023; 18:1401-1408. [PMID: 37653051 DOI: 10.1038/s41565-023-01495-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Patterning antidots, which are regions of potential hills that repel electrons, into well-defined antidot lattices creates fascinating artificial periodic structures, leading to anomalous transport properties and exotic quantum phenomena in two-dimensional systems. Although nanolithography has brought conventional antidots from the semiclassical regime to the quantum regime, achieving precise control over the size of each antidot and its spatial period at the atomic scale has remained challenging. However, attaining such control opens the door to a new paradigm, enabling the creation of quantum antidots with discrete quantum hole states, which, in turn, offer a fertile platform to explore novel quantum phenomena and hot electron dynamics in previously inaccessible regimes. Here we report an atomically precise bottom-up fabrication of a series of atomic-scale quantum antidots through a thermal-induced assembly of a chalcogenide single vacancy in PtTe2. Such quantum antidots consist of highly ordered single-vacancy lattices, spaced by a single Te atom, reaching the ultimate downscaling limit of antidot lattices. Increasing the number of single vacancies in quantum antidots strengthens the cumulative repulsive potential and consequently enhances the collective interference of multiple-pocket scattered quasiparticles inside quantum antidots, creating multilevel quantum hole states with a tunable gap from the telecom to far-infrared regime. Moreover, precisely engineered quantum hole states of quantum antidots are geometry protected and thus survive on oxygen substitutional doping. Therefore, single-vacancy-assembled quantum antidots exhibit unprecedented robustness and property tunability, positioning them as highly promising candidates for advancing quantum information and photocatalysis technologies.
Collapse
Affiliation(s)
- Hanyan Fang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Harshitra Mahalingam
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore
| | - Xinzhe Li
- School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xu Han
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Zhizhan Qiu
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore
| | - Yixuan Han
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Keian Noori
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, Singapore, Singapore
| | | | - Hongfei Chen
- Joint Key Laboratory of Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Taipa, China
| | - Pin Lyu
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Tianhao Yang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Jing Li
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, China
| | - Chenliang Su
- International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, China
| | - Wei Chen
- Department of Chemistry, National University of Singapore, Singapore, Singapore
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, Singapore, Singapore
| | - Yongqing Cai
- Joint Key Laboratory of Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Taipa, China
| | - A H Castro Neto
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, Singapore, Singapore
| | - Kostya S Novoselov
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, Singapore, Singapore
| | - Aleksandr Rodin
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, Singapore, Singapore.
- Yale-NUS College, Singapore, Singapore.
- Materials Science and Engineering, National University of Singapore, Singapore, Singapore.
| | - Jiong Lu
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, Singapore.
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore, Singapore, Singapore.
| |
Collapse
|
29
|
Chow EWL, Song Y, Chen J, Xu X, Wang J, Chen K, Gao J, Wang Y. The transcription factor Rpn4 activates its own transcription and induces efflux pump expression to confer fluconazole resistance in Candida auris. mBio 2023; 14:e0268823. [PMID: 38014938 PMCID: PMC10746192 DOI: 10.1128/mbio.02688-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Candida auris is a recently emerged pathogenic fungus of grave concern globally due to its resistance to conventional antifungals. This study takes a whole-genome approach to explore how C. auris overcomes growth inhibition imposed by the common antifungal drug fluconazole. We focused on gene disruptions caused by a "jumping genetic element" called transposon, leading to fluconazole resistance. We identified mutations in two genes, each encoding a component of the Ubr2/Mub1 ubiquitin-ligase complex, which marks the transcription regulator Rpn4 for degradation. When either protein is absent, stable Rpn4 accumulates in the cell. We found that Rpn4 activates the expression of itself as well as the main drug efflux pump gene CDR1 by binding to a PACE element in the promoter. Furthermore, we identified an amino acid change in Ubr2 in many resistant clinical isolates, contributing to Rpn4 stabilization and increased fluconazole resistance.
Collapse
Affiliation(s)
- Eve W. L. Chow
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yabing Song
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinxin Chen
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Xu
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiaxin Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Wang
- Infectious Diseases Labs, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
30
|
Choo Z, Koh X, Wong MRE, Ashokan RM, Ali Ahamed NSB, Kang C, Kuick CH, Chang KTE, Larisch S, Loh AHP, Chen ZX. Targeted Degradation of XIAP is Sufficient and Specific to Induce Apoptosis in MYCN-overexpressing High-risk Neuroblastoma. Cancer Res Commun 2023; 3:2386-2399. [PMID: 37874199 PMCID: PMC10681007 DOI: 10.1158/2767-9764.crc-23-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/22/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
XIAP, the most potent mammalian inhibitor of apoptosis protein (IAP), critically restricts developmental culling of sympathetic neuronal progenitors, and is correspondingly overexpressed in most MYCN-amplified neuroblastoma tumors. Because apoptosis-related protein in the TGFβ signaling pathway (ARTS) is the only XIAP antagonist that directly binds and degrades XIAP, we evaluated the preclinical effectiveness and tolerability of XIAP antagonism as a novel targeting strategy for neuroblastoma. We found that antagonism of XIAP, but not other IAPs, triggered apoptotic death in neuroblastoma cells. XIAP silencing induced apoptosis while overexpression conferred protection from drug-induced apoptosis. From a screen of IAP inhibitors, first-in-class ARTS mimetic A4 was most effective against high-risk and high XIAP-expressing neuroblastoma cells, and least toxic toward normal liver- and bone marrow-derived cells, compared with pan-IAP antagonists. On target engagement assays and nuclear magnetic resonance spectroscopy, A4 was observed to degrade rather than inhibit XIAP, catalyzing rapid degradation of XIAP through the ubiquitin-proteasome pathway. In MYCN-amplified neuroblastoma patient-derived xenografts, A4 significantly prolonged survival as a single agent, and demonstrated synergism with standard-of-care agents to reduce their effective required doses 3- to 6-fold. Engagement and degradation of XIAP by ARTS mimetics is a novel targeting strategy for neuroblastoma that may be especially effective against MYCN-amplified disease with intrinsically high XIAP expression. First-in-class ARTS mimetic A4 demonstrates preclinical efficacy and warrants further development and study. SIGNIFICANCE XIAP degradation is sufficient to kill MYCN-amplified neuroblastoma which overexpresses and relies on XIAP as a brake against cell death, without affecting normal cells.
Collapse
Affiliation(s)
- Zhang'E Choo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xiaoying Koh
- Experimental Drug Development Centre, A*STAR, Singapore
| | - Megan Rui En Wong
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
| | - Ruth Minothini Ashokan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nurul Suhana Binte Ali Ahamed
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - CongBao Kang
- Experimental Drug Development Centre, A*STAR, Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | - Kenneth Tou En Chang
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
- Duke NUS Medical School, Singapore
| | - Sarit Larisch
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, Israel
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
- Duke NUS Medical School, Singapore
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, Israel
- Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore
| | - Zhi Xiong Chen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore
- National University Cancer Institute, Singapore, National University Health System, Singapore
| |
Collapse
|
31
|
Chen Q, Chia A, Hang SK, Lim A, Koh WK, Peng Y, Gao F, Chen J, Ho Z, Wai LE, Kunasegaran K, Tan AT, Le Bert N, Loh CY, Goh YS, Renia L, Dong T, Vathsala A, Bertoletti A. Engineering immunosuppressive drug-resistant armored (IDRA) SARS-CoV-2 T cells for cell therapy. Cell Mol Immunol 2023; 20:1300-1312. [PMID: 37666955 PMCID: PMC10616128 DOI: 10.1038/s41423-023-01080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Solid organ transplant (SOT) recipients receive immunosuppressive drugs (ISDs) and are susceptible to developing severe COVID-19. Here, we analyze the Spike-specific T-cell response after 3 doses of mRNA vaccine in a group of SOT patients (n = 136) treated with different ISDs. We demonstrate that a combination of a calcineurin inhibitor (CNI), mycophenolate mofetil (MMF), and prednisone (Pred) treatment regimen strongly suppressed the mRNA vaccine-induced Spike-specific cellular response. Such defects have clinical consequences because the magnitude of vaccine-induced Spike-specific T cells was directly proportional to the ability of SOT patients to rapidly clear SARS-CoV-2 after breakthrough infection. To then compensate for the T-cell defects induced by immunosuppressive treatment and to develop an alternative therapeutic strategy for SOT patients, we describe production of 6 distinct SARS-CoV-2 epitope-specific ISD-resistant T-cell receptor (TCR)-T cells engineered using the mRNA electroporation method with reactivity minimally affected by mutations occurring in Beta, Delta, Gamma, and Omicron variants. This strategy with transient expression characteristics marks an improvement in the immunotherapeutic field and provides an attractive and novel therapeutic possibility for immunosuppressed COVID-19 patients.
Collapse
Affiliation(s)
- Qi Chen
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Adeline Chia
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Shou Kit Hang
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Amy Lim
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
| | - Wee Kun Koh
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Fei Gao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jili Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Zack Ho
- Lion TCR Pte Ltd, Singapore, Singapore
| | - Lu-En Wai
- Lion TCR Pte Ltd, Singapore, Singapore
| | - Kamini Kunasegaran
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Anthony Tanoto Tan
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Nina Le Bert
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Chiew Yee Loh
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yun Shan Goh
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Laurent Renia
- A*STAR ID labs, Agency for Science, Technology and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anantharaman Vathsala
- National University Centre for Organ Transplantation, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Antonio Bertoletti
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore.
- Singapore Immunology Network, A*STAR, Singapore, Singapore.
| |
Collapse
|
32
|
Gao S, Li Z, Van Petegem S, Ge J, Goel S, Vas JV, Luzin V, Hu Z, Seet HL, Sanchez DF, Van Swygenhoven H, Gao H, Seita M. Additive manufacturing of alloys with programmable microstructure and properties. Nat Commun 2023; 14:6752. [PMID: 37903769 PMCID: PMC10616214 DOI: 10.1038/s41467-023-42326-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
In metallurgy, mechanical deformation is essential to engineer the microstructure of metals and to tailor their mechanical properties. However, this practice is inapplicable to near-net-shape metal parts produced by additive manufacturing (AM), since it would irremediably compromise their carefully designed geometries. In this work, we show how to circumvent this limitation by controlling the dislocation density and thermal stability of a steel alloy produced by laser powder bed fusion (LPBF) technology. We show that by manipulating the alloy's solidification structure, we can 'program' recrystallization upon heat treatment without using mechanical deformation. When employed site-specifically, our strategy enables designing and creating complex microstructure architectures that combine recrystallized and non-recrystallized regions with different microstructural features and properties. We show how this heterogeneity may be conducive to materials with superior performance compared to those with monolithic microstructure. Our work inspires the design of high-performance metal parts with artificially engineered microstructures by AM.
Collapse
Affiliation(s)
- Shubo Gao
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 639798, Republic of Singapore
- Additive Manufacturing Division, Singapore Institute of Manufacturing Technology (SIMTech), Agency for Science, Technology and Research (A*STAR), Singapore, 636732, Republic of Singapore
| | - Zhi Li
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore, 138632, Republic of Singapore
| | - Steven Van Petegem
- Photon Science Division, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Junyu Ge
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 639798, Republic of Singapore
| | - Sneha Goel
- Photon Science Division, Paul Scherrer Institute, Villigen, 5232, Switzerland
- VTT Technical Research Centre of Finland, Espoo, 02150, Finland
- Advanced materials for nuclear energy, VTT Technical Research Centre of Finland, Espoo, 02150, Finland
| | - Joseph Vimal Vas
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Republic of Singapore
| | - Vladimir Luzin
- Australian Nuclear Science & Technology Organisation (ANSTO), Lucas Heights, NSW, 2234, Australia
| | - Zhiheng Hu
- Additive Manufacturing Division, Singapore Institute of Manufacturing Technology (SIMTech), Agency for Science, Technology and Research (A*STAR), Singapore, 636732, Republic of Singapore
| | - Hang Li Seet
- Additive Manufacturing Division, Singapore Institute of Manufacturing Technology (SIMTech), Agency for Science, Technology and Research (A*STAR), Singapore, 636732, Republic of Singapore
| | | | | | - Huajian Gao
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 639798, Republic of Singapore
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore, 138632, Republic of Singapore
| | - Matteo Seita
- Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK.
| |
Collapse
|
33
|
Wang M, Lin T, Wang L, Lin A, Zou K, Xu X, Zhou Y, Peng Y, Meng Q, Qian Y, Deng G, Wu Z, Chen J, Lin J, Zhang M, Zhu W, Zhang C, Zhang D, Goh RSM, Liu Y, Pang CP, Chen X, Chen H, Fu H. Uncertainty-inspired open set learning for retinal anomaly identification. Nat Commun 2023; 14:6757. [PMID: 37875484 PMCID: PMC10598011 DOI: 10.1038/s41467-023-42444-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
Failure to recognize samples from the classes unseen during training is a major limitation of artificial intelligence in the real-world implementation for recognition and classification of retinal anomalies. We establish an uncertainty-inspired open set (UIOS) model, which is trained with fundus images of 9 retinal conditions. Besides assessing the probability of each category, UIOS also calculates an uncertainty score to express its confidence. Our UIOS model with thresholding strategy achieves an F1 score of 99.55%, 97.01% and 91.91% for the internal testing set, external target categories (TC)-JSIEC dataset and TC-unseen testing set, respectively, compared to the F1 score of 92.20%, 80.69% and 64.74% by the standard AI model. Furthermore, UIOS correctly predicts high uncertainty scores, which would prompt the need for a manual check in the datasets of non-target categories retinal diseases, low-quality fundus images, and non-fundus images. UIOS provides a robust method for real-world screening of retinal anomalies.
Collapse
Affiliation(s)
- Meng Wang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Tian Lin
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, 515041, Shantou, Guangdong, China
| | - Lianyu Wang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 211100, Nanjing, Jiangsu, China
- Laboratory of Brain-Machine Intelligence Technology, Ministry of Education Nanjing University of Aeronautics and Astronautics, 211106, Nanjing, Jiangsu, China
| | - Aidi Lin
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, 515041, Shantou, Guangdong, China
| | - Ke Zou
- National Key Laboratory of Fundamental Science on Synthetic Vision and the College of Computer Science, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Xinxing Xu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Yi Zhou
- School of Electronics and Information Engineering, Soochow University, 215006, Suzhou, Jiangsu, China
| | - Yuanyuan Peng
- School of Biomedical Engineering, Anhui Medical University, 230032, Hefei, Anhui, China
| | - Qingquan Meng
- School of Electronics and Information Engineering, Soochow University, 215006, Suzhou, Jiangsu, China
| | - Yiming Qian
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Guoyao Deng
- National Key Laboratory of Fundamental Science on Synthetic Vision and the College of Computer Science, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Zhiqun Wu
- Longchuan People's Hospital, 517300, Heyuan, Guangdong, China
| | - Junhong Chen
- Puning People's Hospital, 515300, Jieyang, Guangdong, China
| | - Jianhong Lin
- Haifeng PengPai Memory Hospital, 516400, Shanwei, Guangdong, China
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, 515041, Shantou, Guangdong, China
| | - Weifang Zhu
- School of Electronics and Information Engineering, Soochow University, 215006, Suzhou, Jiangsu, China
| | - Changqing Zhang
- College of Intelligence and Computing, Tianjin University, 300350, Tianjin, China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 211100, Nanjing, Jiangsu, China
- Laboratory of Brain-Machine Intelligence Technology, Ministry of Education Nanjing University of Aeronautics and Astronautics, 211106, Nanjing, Jiangsu, China
| | - Rick Siow Mong Goh
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Yong Liu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore
| | - Chi Pui Pang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, 515041, Shantou, Guangdong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, 999077, Hong Kong, China
| | - Xinjian Chen
- School of Electronics and Information Engineering, Soochow University, 215006, Suzhou, Jiangsu, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, 215006, Suzhou, China.
| | - Haoyu Chen
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, 515041, Shantou, Guangdong, China.
| | - Huazhu Fu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Republic of Singapore.
| |
Collapse
|
34
|
Chen S, Liu P, Pei Q, Yu ZG, Aitken ZH, Li W, Wu Z, Banerjee R, Srolovitz DJ, Liaw PK, Zhang YW. Ideal plasticity and shape memory of nanolamellar high-entropy alloys. Sci Adv 2023; 9:eadi5817. [PMID: 37831772 PMCID: PMC10575575 DOI: 10.1126/sciadv.adi5817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
Understanding the relationship among elemental compositions, nanolamellar microstructures, and mechanical properties enables the rational design of high-entropy alloys (HEAs). Here, we construct nanolamellar AlxCoCuFeNi HEAs with alternating high- and low-Al concentration layers and explore their mechanical properties using a combination of molecular dynamic simulation and density functional theory calculation. Our results show that the HEAs with nanolamellar structures exhibit ideal plastic behavior during uniaxial tensile loading, a feature not observed in homogeneous HEAs. This remarkable ideal plasticity is attributed to the unique deformation mechanisms of phase transformation coupled with dislocation nucleation and propagation in the high-Al concentration layers and the confinement and slip-blocking effect of the low-Al concentration layers. Unexpectedly, this ideal plasticity is fully reversible upon unloading, leading to a remarkable shape memory effect. Our work highlights the importance of nanolamellar structures in controlling the mechanical and functional properties of HEAs and presents a fascinating route for the design of HEAs for both functional and structural applications.
Collapse
Affiliation(s)
- Shuai Chen
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| | - Ping Liu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| | - Qingxiang Pei
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| | - Zhi Gen Yu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| | - Zachary H. Aitken
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| | - Wanghui Li
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| | - Zhaoxuan Wu
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong SAR, China
| | - Rajarshi Banerjee
- Department of Materials Science and Engineering, University of North Texas, Denton, TX 76207, USA
| | - David J. Srolovitz
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Peter K. Liaw
- Department of Materials Science and Engineering, The University of Tennessee, Knoxville, TN 37996, USA
| | - Yong-Wei Zhang
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore
| |
Collapse
|
35
|
Robinson KS, Toh GA, Firdaus MJ, Tham KC, Rozario P, Lim CK, Toh YX, Lau ZH, Binder SC, Mayer J, Bonnard C, Schmidt FI, Common JE, Zhong FL. Diphtheria toxin activates ribotoxic stress and NLRP1 inflammasome-driven pyroptosis. J Exp Med 2023; 220:e20230105. [PMID: 37642997 PMCID: PMC10465786 DOI: 10.1084/jem.20230105] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/01/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023] Open
Abstract
The ZAKα-driven ribotoxic stress response (RSR) is activated by ribosome stalling and/or collisions. Recent work demonstrates that RSR also plays a role in innate immunity by activating the human NLRP1 inflammasome. Here, we report that ZAKα and NLRP1 sense bacterial exotoxins that target ribosome elongation factors. One such toxin, diphtheria toxin (DT), the causative agent for human diphtheria, triggers RSR-dependent inflammasome activation in primary human keratinocytes. This process requires iron-mediated DT production in the bacteria, as well as diphthamide synthesis and ZAKα/p38-driven NLRP1 phosphorylation in host cells. NLRP1 deletion abrogates IL-1β and IL-18 secretion by DT-intoxicated keratinocytes, while ZAKα deletion or inhibition additionally limits both pyroptotic and inflammasome-independent non-pyroptotic cell death. Consequently, pharmacologic inhibition of ZAKα is more effective than caspase-1 inhibition at protecting the epidermal barrier in a 3D skin model of cutaneous diphtheria. In summary, these findings implicate ZAKα-driven RSR and the NLRP1 inflammasome in antibacterial immunity and might explain certain aspects of diphtheria pathogenesis.
Collapse
Affiliation(s)
- Kim Samirah Robinson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- The A*STAR Skin Research Labs, Singapore, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | | | | | - Pritisha Rozario
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Chrissie K. Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Ying Xiu Toh
- The A*STAR Skin Research Labs, Singapore, Singapore
| | - Zhi Heng Lau
- The A*STAR Skin Research Labs, Singapore, Singapore
| | | | - Jacob Mayer
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Florian I. Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Franklin L. Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| |
Collapse
|
36
|
Badrtdinov DI, Rodriguez-Fernandez C, Grzeszczyk M, Qiu Z, Vaklinova K, Huang P, Hampel A, Watanabe K, Taniguchi T, Jiong L, Potemski M, Dreyer CE, Koperski M, Rösner M. Dielectric Environment Sensitivity of Carbon Centers in Hexagonal Boron Nitride. Small 2023; 19:e2300144. [PMID: 37329196 DOI: 10.1002/smll.202300144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/01/2023] [Indexed: 06/18/2023]
Abstract
A key advantage of utilizing van-der-Waals (vdW) materials as defect-hosting platforms for quantum applications is the controllable proximity of the defect to the surface or the substrate allowing for improved light extraction, enhanced coupling with photonic elements, or more sensitive metrology. However, this aspect results in a significant challenge for defect identification and characterization, as the defect's properties depend on the the atomic environment. This study explores how the environment can influence the properties of carbon impurity centers in hexagonal boron nitride (hBN). It compares the optical and electronic properties of such defects between bulk-like and few-layer films, showing alteration of the zero-phonon line energies and their phonon sidebands, and enhancements of inhomogeneous broadenings. To disentangle the mechanisms responsible for these changes, including the atomic structure, electronic wavefunctions, and dielectric screening, it combines ab initio calculations with a quantum-embedding approach. By studying various carbon-based defects embedded in monolayer and bulk hBN, it demonstrates that the dominant effect of the change in the environment is the screening of density-density Coulomb interactions between the defect orbitals. The comparative analysis of experimental and theoretical findings paves the way for improved identification of defects in low-dimensional materials and the development of atomic scale sensors for dielectric environments.
Collapse
Affiliation(s)
- Danis I Badrtdinov
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525, AJ Nijmegen, Netherlands
| | | | - Magdalena Grzeszczyk
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, 117544
| | - Zhizhan Qiu
- Department of Chemistry, National University of Singapore, 117543, Singapore
| | - Kristina Vaklinova
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, 117544
| | - Pengru Huang
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, 117544
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 117575, Singapore
- Guangxi Key Laboratory of Information Materials, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Alexander Hampel
- Center for Computational Quantum Physics, Flatiron Institute, 162 5 th Avenue, New York, NY 10010, USA
| | - Kenji Watanabe
- Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, 305-0044, Japan
| | - Takashi Taniguchi
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, 305-0044, Japan
| | - Lu Jiong
- Department of Chemistry, National University of Singapore, 117543, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore, 117546, Singapore
| | - Marek Potemski
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA-EMFL, 25 Av. des Martyrs, 38042, Grenoble, France
- CENTERA Labs, Institute of High Pressure Physics, PAS PL-01-142, Warsaw, Poland
- Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093, Warszawa, Poland
| | - Cyrus E Dreyer
- Center for Computational Quantum Physics, Flatiron Institute, 162 5 th Avenue, New York, NY 10010, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York, 11794-3800, USA
| | - Maciej Koperski
- Institute for Functional Intelligent Materials, National University of Singapore, Singapore, 117544
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 117575, Singapore
| | - Malte Rösner
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525, AJ Nijmegen, Netherlands
| |
Collapse
|
37
|
Bindra AK, Wang D, Zhao Y. Metal-Organic Frameworks Meet Polymers: From Synthesis Strategies to Healthcare Applications. Adv Mater 2023; 35:e2300700. [PMID: 36848594 DOI: 10.1002/adma.202300700] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Metal-organic frameworks (MOFs) have been at the forefront of nanotechnological research for the past decade owing to their high porosity, high surface area, diverse configurations, and controllable chemical structures. They are a rapidly developing class of nanomaterials that are predominantly applied in batteries, supercapacitors, electrocatalysis, photocatalysis, sensors, drug delivery, gas separation, adsorption, and storage. However, the limited functions and unsatisfactory performance of MOFs resulting from their low chemical and mechanical stability hamper further development. Hybridizing MOFs with polymers is an excellent solution to these problems, because polymers-which are soft, flexible, malleable, and processable-can induce unique properties in the hybrids based on those of the two disparate components while retaining their individuality. This review highlights recent advances in the preparation of MOF-polymer nanomaterials. Furthermore, several applications wherein the incorporation of polymers enhances the MOF performance are discussed, such as anticancer therapy, bacterial elimination, imaging, therapeutics, protection from oxidative stress and inflammation, and environmental remediation. Finally, insights from the focus of existing research and design principles for mitigating future challenges are presented.
Collapse
Affiliation(s)
- Anivind Kaur Bindra
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Dongdong Wang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yanli Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| |
Collapse
|
38
|
Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
Collapse
Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
39
|
Graves N, Ganesan G, Tan KB, Goh OQ, Ho J, Chong TT, Bishnoi P, Carmody D, Yuh AS, Ng YZ, Lo Z, Enming Y, Abu Bakar Aloweni F, Zifei W, Harding K. Chronic wounds in a multiethnic Asian population: a cost of illness study. BMJ Open 2023; 13:e065692. [PMID: 37723106 PMCID: PMC10510887 DOI: 10.1136/bmjopen-2022-065692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
OBJECTIVE To estimate the 'cost of illness' arising from chronic wounds in Singapore. DESIGN Incidence-based cost of illness study using evidence from a range of sources. SETTING Singapore health services. PARTICIPANTS We consider 3.49 million Singapore citizens and permanent residents. There are 16 752 new individuals with a chronic wound in 2017, with 598 venous ulcers, 2206 arterial insufficiency ulcers, 6680 diabetic ulcers and 7268 pressure injuries.Primary outcome measures expressed in monetary terms are the value of all hospital bed days lost for the population; monetary value of quality-adjusted life years (QALYs) lost in the population; costs of all outpatient visits; and costs of all poly clinic, use of Community Health Assist Scheme (CHAS) and emergency departments (EDs) visits. Intermediate outcomes that inform the primary outcomes are also estimated. RESULTS Total annual cost of illness was $350 million (range $72-$1779 million). With 168 503 acute bed days taken up annually (range 141 966-196 032) that incurred costs of $139 million (range 117-161 million). Total costs to health services were $184 million (range $120-$1179 million). Total annual costs of lost health outcomes were 2077 QALYs (range -2657 to 29 029) valued at $166 million (range -212 to 2399 million). CONCLUSIONS The costs of chronic wounds are large to Singapore. Costs can be reduced by making positive investments for comprehensive wound prevention and treatment programmes.
Collapse
Affiliation(s)
- Nicholas Graves
- Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Ganga Ganesan
- Health Services Research, Ministry of Health, Singapore
| | - Kelvin Bryan Tan
- SingHealth Duke-NUSGlobal Health Institute, Duke-NUS Medical School, Singapore
| | - Orlanda Qm Goh
- Department of Internal Medicine, Singapore General Hospital, Singapore
| | - Jackie Ho
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tze Tec Chong
- Department of Vascular Surgery, Singapore General Hospital, Singapore
| | - Priya Bishnoi
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research (A*STAR), Singapore
| | - David Carmody
- Department of Endocrinology, Singapore General Hospital, Singapore
| | - Ang Shin Yuh
- Nursing Division, Singapore General Hospital, Singapore
| | - Yi Zhen Ng
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Zhiwen Lo
- Department of Surgery, Vascular Surgery Woodlands Health, Singapore
| | - Yong Enming
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | | | - Wang Zifei
- Skin Research Institute of Singapore (SRIS), Singapore
| | - Keith Harding
- Skin Research Institute of Singapore (SRIS), Singapore
| |
Collapse
|
40
|
Ng AS, Chan DKH. Commonalities and differences in the mutational signature and somatic driver mutation landscape across solid and hollow viscus organs. Oncogene 2023; 42:2713-2724. [PMID: 37573406 PMCID: PMC10491491 DOI: 10.1038/s41388-023-02802-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Advances in sequencing have revealed a highly variegated landscape of mutational signatures and somatic driver mutations in a range of normal tissues. Normal tissues accumulate mutations at varying rates ranging from 11 per cell per year in the liver, to 1879 per cell per year in the bladder. In addition, some normal tissues are also comprised of a large proportion of cells which possess driver mutations while appearing phenotypically normal, as in the oesophagus where a majority of cells harbour driver mutations. Individual tissue proliferation and mutation rate, unique mutagenic stimuli, and local tissue architecture contribute to this highly variegated landscape which confounds the functional characterization of driver mutations found in normal tissue. In particular, our understanding of the relationship between normal tissue somatic mutations and tumour initiation or future cancer risk remains poor. Here, we describe the mutational signatures and somatic driver mutations in solid and hollow viscus organs, highlighting unique characteristics in a tissue-specific manner, while simultaneously seeking to describe commonalities which can bring forward a basic unified theory on the role of these driver mutations in tumour initiation. We discuss novel findings which can be used to inform future research in this field.
Collapse
Affiliation(s)
- Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Dedrick Kok Hong Chan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Division of Colorectal Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
| |
Collapse
|
41
|
Li Z, Ma X, Wei F, Wang D, Deng Z, Jiang M, Siddiquee A, Qi K, Zhu D, Zhao M, Shen M, Canepa P, Kou S, Lin J, Wang Q. As-Grown Miniaturized True Zero-Order Waveplates Based on Low-Dimensional Ferrocene Crystals. Adv Mater 2023; 35:e2302468. [PMID: 37207692 DOI: 10.1002/adma.202302468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/12/2023] [Indexed: 05/21/2023]
Abstract
As basic optical elements, waveplates with anisotropic electromagnetic responses are imperative for manipulating light polarization. Conventional waveplates are manufactured from bulk crystals (e.g., quartz and calcite) through a series of precision cutting and grinding steps, which typically result in large size, low yield, and high cost. In this study, a bottom-up method is used to grow ferrocene crystals with large anisotropy to demonstrate self-assembled ultrathin true zero-order waveplates without additional machining processing, which is particularly suited for nanophotonic integration. The van der Waals ferrocene crystals exhibit high birefringence (Δn (experiment) = 0.149 ± 0.002 at 636 nm), low dichroism Δκ (experiment) = -0.0007 at 636 nm), and a potentially broad operating range (550 nm to 20 µm) as suggested by Density Functional Theory (DFT) calculations. In addition, the grown waveplate's highest and the lowest principal axes (n1 and n3 , respectively) are in the a-c plane, where the fast axis is along one natural edge of the ferrocene crystal, rendering them readily usable. The as-grown, wavelength-scale-thick waveplate allows the development of further miniaturized systems via tandem integration.
Collapse
Affiliation(s)
- Zhipeng Li
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Xuezhi Ma
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Fengxia Wei
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Dapeng Wang
- Institute of Biointelligence Technology, BGI-Research Shenzhen, Shenzhen, 518083, China
| | - Zeyu Deng
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 117575, Singapore
| | - Mengting Jiang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Arif Siddiquee
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Victoria, 3086, Australia
| | - Kun Qi
- Institut Européen des Membranes, IEM, UMR 5635, Université Montpellier, ENSCM, CNRS, Montpellier, 34000, France
| | - Di Zhu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Meng Zhao
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Mengzhe Shen
- Institute of Biointelligence Technology, BGI-Research Shenzhen, Shenzhen, 518083, China
| | - Pieremanuele Canepa
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 117575, Singapore
| | - Shanshan Kou
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Victoria, 3086, Australia
| | - Jiao Lin
- School of Engineering, RMIT University, Victoria, 3000, Australia
| | - Qian Wang
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| |
Collapse
|
42
|
Chu R, Wei Y, Liu J, Li B, Zhang J, Zhou Y, Du Y, Zhang Y. A Variant of the Sulfoglycolytic Transketolase Pathway for the Degradation of Sulfoquinovose into Sulfoacetate. Appl Environ Microbiol 2023; 89:e0061723. [PMID: 37404184 PMCID: PMC10370302 DOI: 10.1128/aem.00617-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Sulfoquinovose (SQ, 6-deoxy-6-sulfo-glucose) constitutes the polar head group of plant sulfolipids and is one of the most abundantly produced organosulfur compounds in nature. Degradation of SQ by bacterial communities contributes to sulfur recycling in many environments. Bacteria have evolved at least four mechanisms for glycolytic degradation of SQ, termed sulfoglycolysis, producing C3 sulfonate (dihydroxypropanesulfonate and sulfolactate) and C2 sulfonate (isethionate) by-products. These sulfonates are further degraded by other bacteria, leading to the mineralization of the sulfonate sulfur. The C2 sulfonate sulfoacetate is widespread in the environment and is also thought to be a product of sulfoglycolysis, although the mechanistic details are yet unknown. Here, we describe a gene cluster in an Acholeplasma sp., from a metagenome derived from deeply circulating subsurface aquifer fluids (GenBank accession no. QZKD01000037), encoding a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway that produces sulfoacetate instead of isethionate as a by-product. We report the biochemical characterization of a coenzyme A (CoA)-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL), which collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria, adding to the variety of mechanisms by which bacteria metabolize this ubiquitous sulfo-sugar. IMPORTANCE Many bacteria utilize environmentally widespread C2 sulfonate sulfoacetate as a sulfur source, and the disease-linked human gut sulfate- and sulfite-reducing bacteria can use it as a terminal electron receptor for anaerobic respiration generating toxic H2S. However, the mechanism of sulfoacetate formation is unknown, although it has been proposed that sulfoacetate originates from bacterial degradation of sulfoquinovose (SQ), the polar head group of sulfolipids present in all green plants. Here, we describe a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway. Unlike the regular sulfo-TK pathway that produces isethionate, our biochemical assays with recombinant proteins demonstrated that a CoA-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL) in this variant pathway collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria and interpreted the widespread existence of sulfoacetate.
Collapse
Affiliation(s)
- Ruoxing Chu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Boran Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianing Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yunfei Du
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
| |
Collapse
|
43
|
Luo W, Cao L, Shi Y, Wan L, Zhang H, Li S, Chen G, Li Y, Li S, Wang Y, Sun S, Karim MF, Cai H, Kwek LC, Liu AQ. Recent progress in quantum photonic chips for quantum communication and internet. Light Sci Appl 2023; 12:175. [PMID: 37443095 DOI: 10.1038/s41377-023-01173-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 07/15/2023]
Abstract
Recent years have witnessed significant progress in quantum communication and quantum internet with the emerging quantum photonic chips, whose characteristics of scalability, stability, and low cost, flourish and open up new possibilities in miniaturized footprints. Here, we provide an overview of the advances in quantum photonic chips for quantum communication, beginning with a summary of the prevalent photonic integrated fabrication platforms and key components for integrated quantum communication systems. We then discuss a range of quantum communication applications, such as quantum key distribution and quantum teleportation. Finally, the review culminates with a perspective on challenges towards high-performance chip-based quantum communication, as well as a glimpse into future opportunities for integrated quantum networks.
Collapse
Affiliation(s)
- Wei Luo
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Lin Cao
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Yuzhi Shi
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, 200092, Shanghai, China.
| | - Lingxiao Wan
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Hui Zhang
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Shuyi Li
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Guanyu Chen
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Yuan Li
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Sijin Li
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore
| | - Yunxiang Wang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Shihai Sun
- School of Electronics and Communication Engineering, Sun Yat-Sen University, 518100, Shenzhen, Guangdong, China
| | - Muhammad Faeyz Karim
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore.
| | - Hong Cai
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), Singapore, 138634, Singapore.
| | - Leong Chuan Kwek
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore.
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore, 117543, Singapore.
- National Institute of Education, Nanyang Technological University, Singapore, 637616, Singapore.
| | - Ai Qun Liu
- Quantum Science and Engineering Centre (QSec), Nanyang Technological University, Singapore, 639798, Singapore.
| |
Collapse
|
44
|
Shen C, Liu C, Qiu A. Metabolism-related brain morphology accelerates aging and predicts neurodegenerative diseases and stroke: a UK Biobank study. Transl Psychiatry 2023; 13:233. [PMID: 37385998 DOI: 10.1038/s41398-023-02515-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023] Open
Abstract
Metabolic syndrome (MetS) is characterized by a constellation of metabolic risk factors, including obesity, hypertriglyceridemia, low high-density lipoprotein (HDL) levels, hypertension, and hyperglycemia, and is associated with stroke and neurodegenerative diseases. This study capitalized on brain structural images and clinical data from the UK Biobank and explored the associations of brain morphology with MetS and brain aging due to MetS. Cortical surface area, thickness, and subcortical volumes were assessed using FreeSurfer. Linear regression was used to examine associations of brain morphology with five MetS components and the MetS severity in a metabolic aging group (N = 23,676, age 62.8 ± 7.5 years). Partial least squares (PLS) were employed to predict brain age using MetS-associated brain morphology. The five MetS components and MetS severity were associated with increased cortical surface area and decreased thickness, particularly in the frontal, temporal, and sensorimotor cortex, and reduced volumes in the basal ganglia. Obesity best explained the variation of brain morphology. Moreover, participants with the most severe MetS had brain age 1-year older than those without MetS. Brain age in patients with stroke (N = 1042), dementia (N = 83), Parkinson's (N = 107), and multiple sclerosis (N = 235) was greater than that in the metabolic aging group. The obesity-related brain morphology had the leading discriminative power. Therefore, the MetS-related brain morphological model can be used for risk assessment of stroke and neurodegenerative diseases. Our findings suggested that prioritizing adjusting obesity among the five metabolic components may be more helpful for improving brain health in aging populations.
Collapse
Affiliation(s)
- Chenye Shen
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Chaoqiang Liu
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Anqi Qiu
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore.
- NUS (Suzhou) Research Institute, National University of Singapore, Suzhou, China.
- Institute of Data Science, National University of Singapore, Singapore, Singapore.
- Department of Health Technology and Informatics, the Hong Kong Polytechnic University, Hung hom, Hong Kong.
- Department of Biomedical Engineering, the Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
45
|
Parikh BH, Blakeley P, Regha K, Liu Z, Yang B, Bhargava M, Wong DSL, Tan QSW, Wong CSW, Wang HF, Al-Mubaarak A, Chou C, Cheung CMG, Lim KL, Barathi VA, Hunziker W, Lingam G, Hu TX, Su X. Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state. Proc Natl Acad Sci U S A 2023; 120:e2214842120. [PMID: 37339216 DOI: 10.1073/pnas.2214842120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/11/2023] [Indexed: 06/22/2023] Open
Abstract
Transplantation of stem cell-derived retinal pigment epithelial (RPE) cells is considered a viable therapeutic option for age-related macular degeneration (AMD). Several landmark Phase I/II clinical trials have demonstrated safety and tolerability of RPE transplants in AMD patients, albeit with limited efficacy. Currently, there is limited understanding of how the recipient retina regulates the survival, maturation, and fate specification of transplanted RPE cells. To address this, we transplanted stem cell-derived RPE into the subretinal space of immunocompetent rabbits for 1 mo and conducted single-cell RNA sequencing analyses on the explanted RPE monolayers, compared to their age-matched in vitro counterparts. We observed an unequivocal retention of RPE identity, and a trajectory-inferred survival of all in vitro RPE populations after transplantation. Furthermore, there was a unidirectional maturation toward the native adult human RPE state in all transplanted RPE, regardless of stem cell resource. Gene regulatory network analysis suggests that tripartite transcription factors (FOS, JUND, and MAFF) may be specifically activated in posttransplanted RPE cells, to regulate canonical RPE signature gene expression crucial for supporting host photoreceptor function, and to regulate prosurvival genes required for transplanted RPE's adaptation to the host subretinal microenvironment. These findings shed insights into the transcriptional landscape of RPE cells after subretinal transplantation, with important implications for cell-based therapy for AMD.
Collapse
Affiliation(s)
- Bhav Harshad Parikh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Paul Blakeley
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kakkad Regha
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Zengping Liu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
| | - Binxia Yang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Mayuri Bhargava
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Department of Ophthalmology, National University Hospital, Singapore 119074, Singapore
| | - Daniel Soo Lin Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Queenie Shu Woon Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Claudine See Wei Wong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Hao Fei Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Abdurrahmaan Al-Mubaarak
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Chai Chou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | | | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Veluchamy Amutha Barathi
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Academic Clinical Program in Ophthalmology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Walter Hunziker
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Gopal Lingam
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Department of Ophthalmology, National University Hospital, Singapore 119074, Singapore
| | - Tim Xiaoming Hu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Xinyi Su
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Department of Ophthalmology, National University Hospital, Singapore 119074, Singapore
- Institute of Health Innovation and Technology, National University of Singapore, Singapore 119276, Singapore
| |
Collapse
|
46
|
Xu C, Ren Z, Zhou H, Zhou J, Ho CP, Wang N, Lee C. Expanding chiral metamaterials for retrieving fingerprints via vibrational circular dichroism. Light Sci Appl 2023; 12:154. [PMID: 37357238 DOI: 10.1038/s41377-023-01186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 06/27/2023]
Abstract
Circular dichroism (CD) spectroscopy has been widely demonstrated for detecting chiral molecules. However, the determination of chiral mixtures with various concentrations and enantiomeric ratios can be a challenging task. To solve this problem, we report an enhanced vibrational circular dichroism (VCD) sensing platform based on plasmonic chiral metamaterials, which presents a 6-magnitude signal enhancement with a selectivity of chiral molecules. Guided by coupled-mode theory, we leverage both in-plane and out-of-plane symmetry-breaking structures for chiral metamaterial design enabled by a two-step lithography process, which increases the near-field coupling strengths and varies the ratio between absorption and radiation loss, resulting in improved chiral light-matter interaction and enhanced molecular VCD signals. Besides, we demonstrate the thin-film sensing process of BSA and β-lactoglobulin proteins, which contain secondary structures α-helix and β-sheet and achieve a limit of detection down to zeptomole level. Furthermore, we also, for the first time, explore the potential of enhanced VCD spectroscopy by demonstrating a selective sensing process of chiral mixtures, where the mixing ratio can be successfully differentiated with our proposed chiral metamaterials. Our findings improve the sensing signal of molecules and expand the extractable information, paving the way toward label-free, compact, small-volume chiral molecule detection for stereochemical and clinical diagnosis applications.
Collapse
Affiliation(s)
- Cheng Xu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117608, Singapore
- Institute of Microelectronics (IME), Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
| | - Zhihao Ren
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117608, Singapore
- Institute of Microelectronics (IME), Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
| | - Hong Zhou
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117608, Singapore
- Institute of Microelectronics (IME), Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
| | - Jingkai Zhou
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117608, Singapore
| | - Chong Pei Ho
- Institute of Microelectronics (IME), Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
| | - Nan Wang
- Institute of Microelectronics (IME), Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore.
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117608, Singapore.
- NUS Graduate School for Integrative Science and Engineering Program (ISEP), National University of Singapore, Singapore, 117456, Singapore.
| |
Collapse
|
47
|
Zhang Z, Chen Y, Chai K, Kang C, Peh SB, Li H, Ren J, Shi X, Han X, Dejoie C, Day SJ, Yang S, Zhao D. Temperature-dependent rearrangement of gas molecules in ultramicroporous materials for tunable adsorption of CO 2 and C 2H 2. Nat Commun 2023; 14:3789. [PMID: 37355678 DOI: 10.1038/s41467-023-39319-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/05/2023] [Indexed: 06/26/2023] Open
Abstract
The interactions between adsorbed gas molecules within porous metal-organic frameworks are crucial to gas selectivity but remain poorly explored. Here, we report the modulation of packing geometries of CO2 and C2H2 clusters within the ultramicroporous CUK-1 material as a function of temperature. In-situ synchrotron X-ray diffraction reveals a unique temperature-dependent reversal of CO2 and C2H2 adsorption affinities on CUK-1, which is validated by gas sorption and dynamic breakthrough experiments, affording high-purity C2H2 (99.95%) from the equimolar mixture of C2H2/CO2 via a one-step purification process. At low temperatures (<253 K), CUK-1 preferentially adsorbs CO2 with both high selectivity (>10) and capacity (170 cm3 g-1) owing to the formation of CO2 tetramers that simultaneously maximize the guest-guest and host-guest interactions. At room temperature, conventionally selective adsorption of C2H2 is observed. The selectivity reversal, structural robustness, and facile regeneration of CUK-1 suggest its potential for producing high-purity C2H2 by temperature-swing sorption.
Collapse
Affiliation(s)
- Zhaoqiang Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore
| | - Yinlin Chen
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK
| | - Kungang Chai
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Chengjun Kang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore
| | - Shing Bo Peh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore
| | - He Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore
| | - Junyu Ren
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore
| | - Xiansong Shi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore
| | - Xue Han
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Catherine Dejoie
- The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS40220 Cedex 9, 38043, Grenoble, France
| | - Sarah J Day
- Diamond Light Source, Harwell Science Campus, Oxfordshire, OX11 0DE, UK
| | - Sihai Yang
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
| | - Dan Zhao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore, Singapore.
| |
Collapse
|
48
|
Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr 2023; 11:e0348322. [PMID: 37199653 PMCID: PMC10269751 DOI: 10.1128/spectrum.03483-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Bats are the reservoir for numerous human pathogens, including coronaviruses. Despite many coronaviruses having descended from bat ancestors, little is known about virus-host interactions and broader evolutionary history involving bats. Studies have largely focused on the zoonotic potential of coronaviruses with few infection experiments conducted in bat cells. To determine genetic changes derived from replication in bat cells and possibly identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cell line. Here, we observed extensive deletions within the spike and open reading frame 4 (ORF4) genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses, but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that did not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon, abrogating spike expression but maintaining infection in bat cells. After passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions among virus subpopulations. Spike-independent infection of human coronavirus 229E may provide an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and known cellular entry receptors. IMPORTANCE Many viruses, including coronaviruses, originated from bats. Yet, we know little about how these viruses switch between hosts and enter human populations. Coronaviruses have succeeded in establishing in humans at least five times, including endemic coronaviruses and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In an approach to identify requirements for host switches, we established a bat cell line and adapted human coronavirus 229E viruses by serial passage. The resulting viruses lost their spike protein but maintained the ability to infect bat cells, but not human cells. Maintenance of 229E viruses in bat cells appears to be independent of a canonical spike receptor match, which in turn might facilitate cross-species transmission in bats.
Collapse
Affiliation(s)
- Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| |
Collapse
|
49
|
Xu G, Zhou X, Yang S, Wu J, Qiu CW. Observation of bulk quadrupole in topological heat transport. Nat Commun 2023; 14:3252. [PMID: 37277349 DOI: 10.1038/s41467-023-39117-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
The quantized bulk quadrupole moment has so far revealed a non-trivial boundary state with lower-dimensional topological edge states and in-gap zero-dimensional corner modes. In contrast to photonic implementations, state-of-the-art strategies for topological thermal metamaterials struggle to achieve such higher-order hierarchical features. This is due to the absence of quantized bulk quadrupole moments in thermal diffusion fundamentally prohibiting possible band topology expansions. Here, we report a recipe for generating quantized bulk quadrupole moments in fluid heat transport and observe the quadrupole topological phases in non-Hermitian thermal systems. Our experiments show that both the real- and imaginary-valued bands exhibit the hierarchical features of bulk, gapped edge and in-gap corner states-in stark contrast to the higher-order states observed only on real-valued bands in classical wave fields. Our findings open up unique possibilities for diffusive metamaterial engineering and establish a playground for multipolar topological physics.
Collapse
Affiliation(s)
- Guoqiang Xu
- Department of Electrical and Computer Engineering, National University of Singapore, Kent Ridge, Singapore, 117583, Singapore
| | - Xue Zhou
- School of Computer Science and Information Engineering, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Shuihua Yang
- Department of Electrical and Computer Engineering, National University of Singapore, Kent Ridge, Singapore, 117583, Singapore
| | - Jing Wu
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Materials Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Cheng-Wei Qiu
- Department of Electrical and Computer Engineering, National University of Singapore, Kent Ridge, Singapore, 117583, Singapore.
| |
Collapse
|
50
|
Zhao Y, Liu X, Chen J, Chen J, Chen J, Fan L, Yang H, Xi S, Shen L, Wang L. Promote electroreduction of CO 2 via catalyst valence state manipulation by surface-capping ligand. Proc Natl Acad Sci U S A 2023; 120:e2218040120. [PMID: 37216512 PMCID: PMC10235936 DOI: 10.1073/pnas.2218040120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/10/2023] [Indexed: 05/24/2023] Open
Abstract
Electrochemical CO2 reduction provides a potential means for synthesizing value-added chemicals over the near equilibrium potential regime, i.e., formate production on Pd-based catalysts. However, the activity of Pd catalysts has been largely plagued by the potential-depended deactivation pathways (e.g., [Formula: see text]-PdH to [Formula: see text]-PdH phase transition, CO poisoning), limiting the formate production to a narrow potential window of 0 V to -0.25 V vs. reversible hydrogen electrode (RHE). Herein, we discovered that the Pd surface capped with polyvinylpyrrolidone (PVP) ligand exhibits effective resistance to the potential-depended deactivations and can catalyze formate production at a much extended potential window (beyond -0.7 V vs. RHE) with significantly improved activity (~14-times enhancement at -0.4 V vs. RHE) compared to that of the pristine Pd surface. Combined results from physical and electrochemical characterizations, kinetic analysis, and first-principle simulations suggest that the PVP capping ligand can effectively stabilize the high-valence-state Pd species (Pdδ+) resulted from the catalyst synthesis and pretreatments, and these Pdδ+ species are responsible for the inhibited phase transition from [Formula: see text]-PdH to [Formula: see text]-PdH, and the suppression of CO and H2 formation. The present study confers a desired catalyst design principle, introducing positive charges into Pd-based electrocatalyst to enable efficient and stable CO2 to formate conversion.
Collapse
Affiliation(s)
- Yilin Zhao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| | - Xiaoqing Liu
- Department of Mechanical Engineering, National University of Singapore, Singapore117575, Singapore
| | - Jingyi Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| | - Junmei Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| | - Jiayi Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| | - Lei Fan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| | - Haozhou Yang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| | - Shibo Xi
- Institute of Sustainability for Chemicals, Energy and Environment, A*STAR, Jurong Island, Singapore627833, Singapore
| | - Lei Shen
- Department of Mechanical Engineering, National University of Singapore, Singapore117575, Singapore
| | - Lei Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore117585, Singapore
| |
Collapse
|