1
|
Ji J, Yu NJ, Kleiner RE. Sequence- and Structure-Specific tRNA Dihydrouridylation by hDUS2. ACS Cent Sci 2024; 10:803-812. [PMID: 38680565 PMCID: PMC11046453 DOI: 10.1021/acscentsci.3c01382] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 05/01/2024]
Abstract
The post-transcriptional reduction of uridine to dihydrouridine (D) by dihydrouridine synthase (DUS) enzymes is among the most ubiquitous transformations in RNA biology. D is found at multiple sites in tRNAs, and studies in yeast have proposed that each of the four eukaryotic DUS enzymes modifies a different site; however, the molecular basis for this exquisite selectivity is unknown, and human DUS enzymes have remained largely uncharacterized. Here we investigate the substrate specificity of human dihydrouridine synthase 2 (hDUS2) using mechanism-based cross-linking with 5-bromouridine (5-BrUrd)-modified oligonucleotide probes and in vitro dihydrouridylation assays. We find that hDUS2 exclusively modifies U20 across diverse tRNA substrates and identify a minimal GU sequence within the tRNA D loop that underlies selective substrate modification. Further, we use our mechanism-based platform to screen small molecule inhibitors of hDUS2, a potential anticancer target. Our work elucidates the principles of substrate modification by a conserved DUS and provides a general platform for studying RNA modifying enzymes with sequence-defined activity-based probes.
Collapse
Affiliation(s)
- Jingwei Ji
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Nathan J. Yu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
2
|
Wille M, Atkinson R, Barr IG, Burgoyne C, Bond AL, Boyle D, Christie M, Dewar M, Douglas T, Fitzwater T, Hassell C, Jessop R, Klaassen H, Lavers JL, Leung KK, Ringma J, Sutherland DR, Klaassen M. Long-Distance Avian Migrants Fail to Bring 2.3.4.4b HPAI H5N1 Into Australia for a Second Year in a Row. Influenza Other Respir Viruses 2024; 18:e13281. [PMID: 38556461 PMCID: PMC10982072 DOI: 10.1111/irv.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Affiliation(s)
- Michelle Wille
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityThe University of MelbourneMelbourneVictoriaAustralia
- WHO Collaborating Centre for Reference and Research on InfluenzaPeter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | | | - Ian G. Barr
- WHO Collaborating Centre for Reference and Research on InfluenzaPeter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityThe University of MelbourneMelbourneVictoriaAustralia
| | - Charlotte Burgoyne
- Northern Australia Quarantine StrategyDepartment of Agriculture, Fisheries and ForestryCanberraAustralian Capital TerritoryAustralia
| | | | - David Boyle
- Victorian Ornithological Research Group Inc.LeopoldVictoriaAustralia
| | - Maureen Christie
- Victorian Wader Study GroupMelbourneVictoriaAustralia
- Australasian Wader Studies GroupMelbourneVictoriaAustralia
- Friends of Shorebirds SECarpenter RocksSouth AustraliaAustralia
| | - Meagan Dewar
- Future Regions Research CentreFederation University AustraliaBerwickVictoriaAustralia
| | - Tegan Douglas
- Australasian Wader Studies GroupMelbourneVictoriaAustralia
- BirdLife AustraliaMelbourneVictoriaAustralia
| | - Teagan Fitzwater
- Northern Australia Quarantine StrategyDepartment of Agriculture, Fisheries and ForestryCanberraAustralian Capital TerritoryAustralia
| | - Chris Hassell
- Australasian Wader Studies GroupMelbourneVictoriaAustralia
- Global Flyway NetworkBroomeWestern AustraliaAustralia
| | - Roz Jessop
- Victorian Wader Study GroupMelbourneVictoriaAustralia
- Australasian Wader Studies GroupMelbourneVictoriaAustralia
| | - Hiske Klaassen
- School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Jennifer L. Lavers
- Bird GroupThe Natural History MuseumTringUK
- Esperance Tjaltjraak Native Title Aboriginal CorporationEsperanceWestern AustraliaAustralia
- Gulbali InstituteCharles Sturt UniversityWagga WaggaNew South WalesAustralia
| | | | | | - Duncan R. Sutherland
- Phillip Island Nature ParksCowesVictoriaAustralia
- School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Marcel Klaassen
- Victorian Wader Study GroupMelbourneVictoriaAustralia
- Australasian Wader Studies GroupMelbourneVictoriaAustralia
- School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| |
Collapse
|
3
|
Clune-Taylor C. Arguments for a ban on pediatric intersex surgery: A dis/analogy with Jehovah witness blood transfusion. Bioethics 2024. [PMID: 38470400 DOI: 10.1111/bioe.13280] [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: 07/13/2023] [Revised: 01/28/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024]
Abstract
This article argues for a ban on the performance of medically unnecessary genital normalizing surgeries as part of assigning a binary sex/gender to infants with intersex conditions on the basis of autonomy, regardless of etiology. It does this via a dis/analogy with the classic case in bioethics of Jehovah Witness (JW) parents' inability to refuse life-saving blood transfusions for their minor children. Both cases address ethical medical practice in situations where parents are making irreversible medical decisions on the basis of values strongly held, identity, and relationship-shaping values-such as religious beliefs or beliefs regarding the inherent value of binary sex/gender-amidst ethical pluralism. Furthermore, it takes seriously-as we must in the intersex case-that the restriction of parents' right to choose will likely result in serious harms to potentially large percentage of patients, their families, and their larger communities. I address the objection that parents' capacity to choose is restricted in the JW case on the basis of the harm principle or a duty to nonmaleficence, given that the result of parent choice would be death. I provide evidence that this is mistaken from how we treat epistemic uncertainty in the JW case and from cases in which clinicians are ethically obligated to restrict the autonomy of nonminor patients. I conclude that we restrict the parents' right to choose in the JW case-and should in the case of pediatric intersex surgery-to secure patient's future autonomy.
Collapse
Affiliation(s)
- Catherine Clune-Taylor
- Program in Gender and Sexuality Studies, Princeton University, Princeton, New Jersey, USA
| |
Collapse
|
4
|
Goranov AI, Chen H, Duan J, Myneni SCB, Hatcher PG. Potentially Massive and Global Non-Pyrogenic Production of Condensed "Black" Carbon through Biomass Oxidation. Environ Sci Technol 2024; 58:2750-2761. [PMID: 38294931 PMCID: PMC10867845 DOI: 10.1021/acs.est.3c05448] [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] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
With the increased occurrences of wildfires worldwide, there has been an increase in scientific interest surrounding the chemistry of fire-derived "black" carbon (BC). Traditionally, wildfire research has assumed that condensed aromatic carbon (ConAC) is exclusively produced via combustion, and thus, ConAC is equated to BC. However, the lack of correlations between ConAC in soils or rivers and wildfire history suggests that ConAC may be produced non-pyrogenically. Here, we show quantitative evidence that this occurs during the oxidation of biomass with environmentally ubiquitous hydroxyl radicals. Pine wood boards exposed to iron nails and natural weather conditions for 12 years yielded a charcoal-like ConAC-rich material. ConAC was also produced during laboratory oxidations of pine, maple, and brown-rotted oak woods, as well as algae, corn root, and tree bark. Back-of-the-envelope calculations suggest that biomass oxidation could be producing massive non-pyrogenic ConAC fluxes to terrestrial and aquatic environments. These estimates (e.g., 163-182 Tg-ConAC/year to soils) are much higher than the estimated pyrogenic "BC" fluxes (e.g., 128 Tg-ConAC/year to soils) implying that environmental ConAC is primarily non-pyrogenic. This novel perspective suggests that wildfire research trajectories should shift to assessing non-pyrogenic ConAC sources and fluxes, developing new methods for quantifying true BC, and establishing a new view of ConAC as an intermediate species in the biogeochemical processing of biomass during soil humification, aquatic photochemistry, microbial degradation, or mineral-organic matter interactions. We also advise against using BC or pyrogenic carbon (pyC) terminologies for ConAC measured in environmental matrices, unless a pyrogenic source can be confidently assigned.
Collapse
Affiliation(s)
- Aleksandar I. Goranov
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529 United States
| | - Hongmei Chen
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529 United States
| | - Jianshu Duan
- Department
of Geosciences, Princeton University, Princeton, New Jersey 08544 United States
| | - Satish C. B. Myneni
- Department
of Geosciences, Princeton University, Princeton, New Jersey 08544 United States
| | - Patrick G. Hatcher
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529 United States
| |
Collapse
|
5
|
Langer DL, Oh S, Stache EE. Selective poly(vinyl ether) upcycling via photooxidative degradation with visible light. Chem Sci 2024; 15:1840-1845. [PMID: 38303945 PMCID: PMC10829002 DOI: 10.1039/d3sc05613a] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
Poly(vinyl ethers) (PVEs) have many applications, such as adhesives, lubricants, and anticorrosive agents, thanks to their elastic, nonirritating, and chemically inert properties. The recycling of PVEs remains largely underexplored, and current methods lack generality towards other polymer classes. Thus, the chemical upcycling of PVE into small molecule feedstocks would provide an alternative approach to combat these current issues. Here, we report a visible light-mediated method of upcycling poly(isobutyl vinyl ether) (PIBVE) into small molecules via photooxidative degradation using chlorine or bromine radicals. PIBVE can be degraded to low molecular weight oligomers within 2 h, producing good yields of alcohols, aldehydes, and carboxylic acids. Mechanistic studies suggest that hydrogen atom transfer (HAT) from the backbone or the side chain leads to small molecule generation via oxidative cleavages. Additionally, this protocol was applied to a copolymer of poly(methyl acrylate-co-isobutyl vinyl ether) to demonstrate the preference for the degradation of polymers bearing more electron-rich C-H bonds through a judicious choice of abstraction agent. Ultimately, we show that photooxidative degradation enables the selective chemical upcycling of PVEs as a method of plastic waste valorization.
Collapse
Affiliation(s)
- Darren L Langer
- Department of Chemistry and Chemical Biology, Cornell University Ithaca New York 14853 USA
| | - Sewon Oh
- Department of Chemistry and Chemical Biology, Cornell University Ithaca New York 14853 USA
| | - Erin E Stache
- Department of Chemistry and Chemical Biology, Cornell University Ithaca New York 14853 USA
- Department of Chemistry, Princeton University Princeton New Jersey 08544 USA
| |
Collapse
|
6
|
Amormino P, Mercier B, Inbar Y. Anticipated affect predicts moral praise and character judgments. J Pers Soc Psychol 2024:2024-42934-001. [PMID: 38206852 DOI: 10.1037/pspa0000377] [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] [Indexed: 01/13/2024]
Abstract
In four preregistered studies (total N = 5,067), we investigated whether people use their own anticipated affective responses to a situation to make judgments about the praiseworthiness of helping and the moral character of helpers. We found that helpers in more affectively arousing scenarios were seen as more morally motivated, received greater praise, and were seen as having more positive moral character, even when controlling for the perceived benefits of helping. Describing helpers as unemotional reduced the effect of observers' anticipated affect on character judgments. These results suggest that when making praise and character judgments, people not only consider the consequences of a helper's actions but also the emotions they experience when engaging in them-and that they use their own anticipated emotional experience to do this. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
Collapse
Affiliation(s)
| | | | - Yoel Inbar
- Department of Psychology, University of Toronto
| |
Collapse
|
7
|
Omufwoko KS, Cronin AL, Nguyen TTH, Webb AE, Traniello IM, Kocher SD. Developmental transcriptomes predict adult social behaviours in the socially flexible sweat bee, Lasioglossum baleicum. Mol Ecol 2023:e17244. [PMID: 38108560 DOI: 10.1111/mec.17244] [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] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Natural variation can provide important insights into the genetic and environmental factors that shape social behaviour and its evolution. The sweat bee, Lasioglossum baleicum, is a socially flexible bee capable of producing both solitary and eusocial nests. We demonstrate that within a single nesting aggregation, soil temperatures are a strong predictor of the social structure of nests. Sites with warmer temperatures in the spring have a higher frequency of social nests than cooler sites, perhaps because warmer temperatures provide a longer reproductive window for those nests. To identify the molecular correlates of this behavioural variation, we generated a de novo genome assembly for L. baleicum, and we used transcriptomic profiling to compare adults and developing offspring from eusocial and solitary nests. We find that adult, reproductive females have similar expression profiles regardless of social structure in the nest, but that there are strong differences between reproductive females and workers from social nests. We also find substantial differences in the transcriptomic profiles of stage-matched pupae from warmer, social-biased sites compared to cooler, solitary-biased sites. These transcriptional differences are strongly predictive of adult reproductive state, suggesting that the developmental environment may set the stage for adult behaviours in L. baleicum. Together, our results help to characterize the molecular mechanisms shaping variation in social behaviour and highlight a potential role of environmental tuning during development as a factor shaping adult behaviour and physiology in this socially flexible bee.
Collapse
Affiliation(s)
- Kennedy S Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Adam L Cronin
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Thi Thu Ha Nguyen
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Andrew E Webb
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey, USA
| | - Ian M Traniello
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey, USA
| |
Collapse
|
8
|
Boele HJ, Jung C, Sherry S, Roggeveen LEM, Dijkhuizen S, Öhman J, Abraham E, Uvarov A, Boele CP, Gultig K, Rasmussen A, Vinueza-Veloz MF, Medina JF, Koekkoek SKE, De Zeeuw CI, Wang SSH. Accessible and reliable neurometric testing in humans using a smartphone platform. Sci Rep 2023; 13:22871. [PMID: 38129487 PMCID: PMC10739701 DOI: 10.1038/s41598-023-49568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023] Open
Abstract
Tests of human brain circuit function typically require fixed equipment in lab environments. We have developed a smartphone-based platform for neurometric testing. This platform, which uses AI models like computer vision, is optimized for at-home use and produces reproducible, robust results on a battery of tests, including eyeblink conditioning, prepulse inhibition of acoustic startle response, and startle habituation. This approach provides a scalable, universal resource for quantitative assays of central nervous system function.
Collapse
Affiliation(s)
- H J Boele
- Princeton Neuroscience Institute, Princeton, USA.
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands.
| | - C Jung
- Princeton Neuroscience Institute, Princeton, USA
| | - S Sherry
- Princeton Neuroscience Institute, Princeton, USA
| | - L E M Roggeveen
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
- Department of Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - S Dijkhuizen
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - J Öhman
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - E Abraham
- Princeton Neuroscience Institute, Princeton, USA
| | | | - C P Boele
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - K Gultig
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - A Rasmussen
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - M F Vinueza-Veloz
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
- Department of Community Medicine and Global Health, University of Oslo, Oslo, Norway
| | - J F Medina
- Department of Neuroscience, Baylor College of Medicine, Houston, USA
| | - S K E Koekkoek
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
| | - C I De Zeeuw
- Department of Neuroscience, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - S S-H Wang
- Princeton Neuroscience Institute, Princeton, USA.
| |
Collapse
|
9
|
Abate SY, Qi Y, Zhang Q, Jha S, Zhang H, Ma G, Gu X, Wang K, Patton D, Dai Q. Eco-Friendly Solvent Engineered CsPbI 2.77 Br 0.23 Ink for Large-Area and Scalable High Performance Perovskite Solar Cells. Adv Mater 2023:e2310279. [PMID: 38088488 DOI: 10.1002/adma.202310279] [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: 10/04/2023] [Revised: 12/09/2023] [Indexed: 12/20/2023]
Abstract
The performance of large-area perovskite solar cells (PSCs) has been assessed for typical compositions, such as methylammonium lead iodide (MAPbI3 ), using a blade coater, slot-die coater, solution shearing, ink-jet printing, and thermal evaporation. However, the fabrication of large-area all-inorganic perovskite films is not well developed. This study develops, for the first time, an eco-friendly solvent engineered all-inorganic perovskite ink of dimethyl sulfoxide (DMSO) as a main solvent with the addition of acetonitrile (ACN), 2-methoxyethanol (2-ME), or a mixture of ACN and 2-ME to fabricate large-area CsPbI2.77 Br0.23 films with slot-die coater at low temperatures (40-50 °C). The perovskite phase, morphology, defect density, and optoelectrical properties of prepared with different solvent ratios are thoroughly examined and they are correlated with their respective colloidal size distribution and solar cell performance. The optimized slot-die-coated CsPbI2.77 Br0.23 perovskite film, which is prepared from the eco-friendly binary solvents dimethyl sulfoxide:acetonitrile (0.8:0.2 v/v), demonstrates an impressive power conversion efficiency (PCE) of 19.05%. Moreover, the device maintains ≈91% of its original PCE after 1 month at 20% relative humidity in the dark. It is believed that this study will accelerate the reliable manufacturing of perovskite devices.
Collapse
Affiliation(s)
- Seid Yimer Abate
- Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA
| | - Yifang Qi
- Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA
| | - Qiqi Zhang
- Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA
| | - Surabhi Jha
- School of Polymer Science and Engineering, Center for Optoelectronic Materials and Devices, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Haixin Zhang
- Department of Physics, University of Miami, Goral Gables, FL, 33124, USA
- Department of Physics and Astronomy, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Guorong Ma
- School of Polymer Science and Engineering, Center for Optoelectronic Materials and Devices, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Xiaodan Gu
- School of Polymer Science and Engineering, Center for Optoelectronic Materials and Devices, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Kun Wang
- Department of Physics, University of Miami, Goral Gables, FL, 33124, USA
- Department of Physics and Astronomy, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Derek Patton
- School of Polymer Science and Engineering, Center for Optoelectronic Materials and Devices, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Qilin Dai
- Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS, 39217, USA
| |
Collapse
|
10
|
Xu X, Eatmon YL, Christie KSS, McGaughey AL, Guillomaitre N, Datta SS, Ren ZJ, Arnold C, Priestley RD. Tough and Recyclable Phase-Separated Supramolecular Gels via a Dehydration-Hydration Cycle. JACS Au 2023; 3:2772-2779. [PMID: 37885595 PMCID: PMC10598558 DOI: 10.1021/jacsau.3c00326] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023]
Abstract
Hydrogels are compelling materials for emerging applications including soft robotics and autonomous sensing. Mechanical stability over an extensive range of environmental conditions and considerations of sustainability, both environmentally benign processing and end-of-life use, are enduring challenges. To make progress on these challenges, we designed a dehydration-hydration approach to transform soft and weak hydrogels into tough and recyclable supramolecular phase-separated gels (PSGs) using water as the only solvent. The dehydration-hydration approach led to phase separation and the formation of domains consisting of strong polymer-polymer interactions that are critical for forming PSGs. The phase-separated segments acted as robust, physical cross-links to strengthen PSGs, which exhibited enhanced toughness and stretchability in its fully swollen state. PSGs are not prone to overswelling or severe shrinkage in wet conditions and show environmental tolerance in harsh conditions, e.g., solutions with pH between 1 and 14. Finally, we demonstrate the use of PSGs as strain sensors in air and aqueous environments.
Collapse
Affiliation(s)
- Xiaohui Xu
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Yannick L. Eatmon
- Department
of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Kofi S. S. Christie
- Department
of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Andlinger
Center for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Allyson L. McGaughey
- Department
of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Andlinger
Center for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Néhémie Guillomaitre
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Department
of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Sujit S. Datta
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Zhiyong Jason Ren
- Department
of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Andlinger
Center for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Craig Arnold
- Department
of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Rodney D. Priestley
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Princeton
Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08540, United States
| |
Collapse
|
11
|
Chen YT, Yang H, Chu JW. Mechanical codes of chemical-scale specificity in DNA motifs. Chem Sci 2023; 14:10155-10166. [PMID: 37772098 PMCID: PMC10529945 DOI: 10.1039/d3sc01671d] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023] Open
Abstract
In gene transcription, certain sequences of double-stranded (ds)DNA play a vital role in nucleosome positioning and expression initiation. That dsDNA is deformed to various extents in these processes leads us to ask: Could the genomic DNA also have sequence specificity in its chemical-scale mechanical properties? We approach this question using statistical machine learning to determine the rigidity between DNA chemical moieties. What emerges for the polyA, polyG, TpA, and CpG sequences studied here is a unique trigram that contains the quantitative mechanical strengths between bases and along the backbone. In a way, such a sequence-dependent trigram could be viewed as a DNA mechanical code. Interestingly, we discover a compensatory competition between the axial base-stacking interaction and the transverse base-pairing interaction, and such a reciprocal relationship constitutes the most discriminating feature of the mechanical code. Our results also provide chemical-scale understanding for experimental observables. For example, the long polyA persistence length is shown to have strong base stacking while its complement (polyAc) exhibits high backbone rigidity. The mechanical code concept enables a direct reading of the physical interactions encoded in the sequence which, with further development, is expected to shed new light on DNA allostery and DNA-binding drugs.
Collapse
Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| |
Collapse
|
12
|
Dunlap JH, Ethier JG, Putnam-Neeb AA, Iyer S, Luo SXL, Feng H, Garrido Torres JA, Doyle AG, Swager TM, Vaia RA, Mirau P, Crouse CA, Baldwin LA. Continuous flow synthesis of pyridinium salts accelerated by multi-objective Bayesian optimization with active learning. Chem Sci 2023; 14:8061-8069. [PMID: 37538827 PMCID: PMC10395269 DOI: 10.1039/d3sc01303k] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023] Open
Abstract
We report a human-in-the-loop implementation of the multi-objective experimental design via a Bayesian optimization platform (EDBO+) towards the optimization of butylpyridinium bromide synthesis under continuous flow conditions. The algorithm simultaneously optimized reaction yield and production rate (or space-time yield) and generated a well defined Pareto front. The versatility of EDBO+ was demonstrated by expanding the reaction space mid-campaign by increasing the upper temperature limit. Incorporation of continuous flow techniques enabled improved control over reaction parameters compared to common batch chemistry processes, while providing a route towards future automated syntheses and improved scalability. To that end, we applied the open-source Python module, nmrglue, for semi-automated nuclear magnetic resonance (NMR) spectroscopy analysis, and compared the acquired outputs against those obtained through manual processing methods from spectra collected on both low-field (60 MHz) and high-field (400 MHz) NMR spectrometers. The EDBO+ based model was retrained with these four different datasets and the resulting Pareto front predictions provided insight into the effect of data analysis on model predictions. Finally, quaternization of poly(4-vinylpyridine) with bromobutane illustrated the extension of continuous flow chemistry to synthesize functional materials.
Collapse
Affiliation(s)
- John H Dunlap
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
- UES, Inc. Dayton OH 45431 USA
| | - Jeffrey G Ethier
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
- UES, Inc. Dayton OH 45431 USA
| | - Amelia A Putnam-Neeb
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
- National Research Council Research Associate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Sanjay Iyer
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - Shao-Xiong Lennon Luo
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Haosheng Feng
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | | | - Abigail G Doyle
- Department of Chemistry and Biochemistry, University of California Los Angeles CA 90095 USA
| | - Timothy M Swager
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Richard A Vaia
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Peter Mirau
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Christopher A Crouse
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Luke A Baldwin
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| |
Collapse
|
13
|
Eichler CE, Li H, Grunberg ME, Gavis ER. Localization of oskar mRNA by agglomeration in ribonucleoprotein granules. PLoS Genet 2023; 19:e1010877. [PMID: 37624861 PMCID: PMC10484445 DOI: 10.1371/journal.pgen.1010877] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/07/2023] [Accepted: 07/19/2023] [Indexed: 08/27/2023] Open
Abstract
Localization of oskar mRNA to the posterior of the Drosophila oocyte is essential for abdominal patterning and germline development. oskar localization is a multi-step process involving temporally and mechanistically distinct transport modes. Numerous cis-acting elements and trans-acting factors have been identified that mediate earlier motor-dependent transport steps leading to an initial accumulation of oskar at the posterior. Little is known, however, about the requirements for the later localization phase, which depends on cytoplasmic flows and results in the accumulation of large oskar ribonucleoprotein granules, called founder granules, by the end of oogenesis. Using super-resolution microscopy, we show that founder granules are agglomerates of smaller oskar transport particles. In contrast to the earlier kinesin-dependent oskar transport, late-phase localization depends on the sequence as well as on the structure of the spliced oskar localization element (SOLE), but not on the adjacent exon junction complex deposition. Late-phase localization also requires the oskar 3' untranslated region (3' UTR), which targets oskar to founder granules. Together, our results show that 3' UTR-mediated targeting together with SOLE-dependent agglomeration leads to accumulation of oskar in large founder granules at the posterior of the oocyte during late stages of oogenesis. In light of previous work showing that oskar transport particles are solid-like condensates, our findings indicate that founder granules form by a process distinct from that of well-characterized ribonucleoprotein granules like germ granules, P bodies, and stress granules. Additionally, they illustrate how an individual mRNA can be adapted to exploit different localization mechanisms depending on the cellular context.
Collapse
Affiliation(s)
- Catherine E. Eichler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Hui Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Michelle E. Grunberg
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
14
|
Saad-Roy CM, Morris SE, Baker RE, Farrar J, Graham AL, Levin SA, Wagner CE, Metcalf CJE, Grenfell BT. Medium-term scenarios of COVID-19 as a function of immune uncertainties and chronic disease. J R Soc Interface 2023; 20:20230247. [PMID: 37643641 PMCID: PMC10465195 DOI: 10.1098/rsif.2023.0247] [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: 04/25/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023] Open
Abstract
As the SARS-CoV-2 trajectory continues, the longer-term immuno-epidemiology of COVID-19, the dynamics of Long COVID, and the impact of escape variants are important outstanding questions. We examine these remaining uncertainties with a simple modelling framework that accounts for multiple (antigenic) exposures via infection or vaccination. If immunity (to infection or Long COVID) accumulates rapidly with the valency of exposure, we find that infection levels and the burden of Long COVID are markedly reduced in the medium term. More pessimistic assumptions on host adaptive immune responses illustrate that the longer-term burden of COVID-19 may be elevated for years to come. However, we also find that these outcomes could be mitigated by the eventual introduction of a vaccine eliciting robust (i.e. durable, transmission-blocking and/or 'evolution-proof') immunity. Overall, our work stresses the wide range of future scenarios that still remain, the importance of collecting real-world epidemiological data to identify likely outcomes, and the crucial need for the development of a highly effective transmission-blocking, durable and broadly protective vaccine.
Collapse
Affiliation(s)
- Chadi M. Saad-Roy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Sinead E. Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Rachel E. Baker
- Department of Epidemiology, Brown University, Providence, RI, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI, USA
| | | | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - C. Jessica. E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| |
Collapse
|
15
|
Liu Y, Cafiero TR, Park D, Biswas A, Winer BY, Cho CH, Bram Y, Chandar V, Connell AKO, Gertje HP, Crossland N, Schwartz RE, Ploss A. Targeted viral adaptation generates a simian-tropic hepatitis B virus that infects marmoset cells. Nat Commun 2023; 14:3582. [PMID: 37328459 PMCID: PMC10276007 DOI: 10.1038/s41467-023-39148-3] [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: 10/19/2022] [Accepted: 05/26/2023] [Indexed: 06/18/2023] Open
Abstract
Hepatitis B virus (HBV) only infects humans and chimpanzees, posing major challenges for modeling HBV infection and chronic viral hepatitis. The major barrier in establishing HBV infection in non-human primates lies at incompatibilities between HBV and simian orthologues of the HBV receptor, sodium taurocholate co-transporting polypeptide (NTCP). Through mutagenesis analysis and screening among NTCP orthologues from Old World monkeys, New World monkeys and prosimians, we determined key residues responsible for viral binding and internalization, respectively and identified marmosets as a suitable candidate for HBV infection. Primary marmoset hepatocytes and induced pluripotent stem cell-derived hepatocyte-like cells support HBV and more efficient woolly monkey HBV (WMHBV) infection. Adapted chimeric HBV genome harboring residues 1-48 of WMHBV preS1 generated here led to a more efficient infection than wild-type HBV in primary and stem cell derived marmoset hepatocytes. Collectively, our data demonstrate that minimal targeted simianization of HBV can break the species barrier in small NHPs, paving the path for an HBV primate model.
Collapse
Affiliation(s)
- Yongzhen Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Thomas R Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Debby Park
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Research Computing, Office of Information Technology, Princeton University, Princeton, NJ, 08544, USA
| | - Benjamin Y Winer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | | | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Vasuretha Chandar
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Aoife K O' Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Nicholas Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|
16
|
Guo Y, Zhou M, Peng L, Yang J, Li M, Tian J, Chen L, Mauzerall DL. Carbon Mitigation and Environmental Co-Benefits of a Clean Energy Transition in China's Industrial Parks. Environ Sci Technol 2023; 57:6494-6505. [PMID: 37040514 PMCID: PMC10135412 DOI: 10.1021/acs.est.2c05725] [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] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Industrial parks are emerging priorities for carbon mitigation. Here we analyze air quality, human health, and freshwater conservation co-benefits of decarbonizing the energy supply of 850 China's industrial parks. We examine a clean energy transition including early retirement of coal-fired facilities and subsequent replacement with grid electricity and onsite energy alternatives (municipal solid waste-to-energy, rooftop photovoltaic, and distributed wind power). We find that such a transition would reduce greenhouse gas emissions by 41% (equal to 7% of 2014 national CO2 equivalent emissions); emissions of SO2 by 41%, NOx by 32%, and PM2.5 by 43% and freshwater consumption by 20%, relative to a 2030 baseline scenario. Based on modeled air pollutant concentrations, we estimate such a clean energy transition will result in ∼42,000 avoided premature deaths annually due to reduced ambient PM2.5 and ozone exposure. Costs and benefits are monetized including technical costs of changes in equipment and energy use and societal benefits resulting from improvements in human health and reductions of climate impacts. We find that decarbonizing industrial parks brings annual economic benefits of US$30-156 billion in 2030. A clean energy transition in China's industrial parks thus provides both environmental and economic benefits.
Collapse
Affiliation(s)
- Yang Guo
- Princeton
School of Public and International Affairs, Princeton University, Princeton, New Jersey 08544, United States
- School
of Environment, Tsinghua University, Beijing 100084, China
| | - Mi Zhou
- Princeton
School of Public and International Affairs, Princeton University, Princeton, New Jersey 08544, United States
- Laboratory
for Climate and Ocean-Atmosphere Studies, Department of Atmospheric
and Oceanic Sciences, School of Physics, Peking University, Beijing 100871, China
| | - Liqun Peng
- Princeton
School of Public and International Affairs, Princeton University, Princeton, New Jersey 08544, United States
| | - Juhua Yang
- Electric
Power Construction Techno-Economic Consulting Center, China Huadian Corporation Ltd, Beijing 100031, China
| | - Mingwei Li
- Princeton
School of Public and International Affairs, Princeton University, Princeton, New Jersey 08544, United States
| | - Jinping Tian
- School
of Environment, Tsinghua University, Beijing 100084, China
| | - Lyujun Chen
- School
of Environment, Tsinghua University, Beijing 100084, China
| | - Denise L. Mauzerall
- Princeton
School of Public and International Affairs, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
17
|
Thokkadam A, Do T, Ran X, Brynildsen MP, Yang ZJ, Link AJ. High-Throughput Screen Reveals the Structure-Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin. ACS Cent Sci 2023; 9:540-550. [PMID: 36968541 PMCID: PMC10037499 DOI: 10.1021/acscentsci.2c01487] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 06/16/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of bacteria including opportunistic human pathogens. Immunocompromised individuals and cystic fibrosis patients are especially vulnerable to serious infections by these bacteria, motivating the search for compounds with antimicrobial activity against the Bcc. Ubonodin is a lasso peptide with promising activity against Bcc species, working by inhibiting RNA polymerase in susceptible bacteria. We constructed a library of over 90 000 ubonodin variants with 2 amino acid substitutions and used a high-throughput screen and next-generation sequencing to examine the fitness of the entire library, generating the most comprehensive data set on lasso peptide activity so far. This screen revealed information regarding the structure-activity relationship of ubonodin over a large sequence space. Remarkably, the screen identified one variant with not only improved activity compared to wild-type ubonodin but also a submicromolar minimum inhibitory concentration (MIC) against a clinical isolate of the Bcc member Burkholderia cenocepacia. Ubonodin and several of the variants identified in this study had lower MICs against certain Bcc strains than those of many clinically approved antibiotics. Finally, the large library size enabled us to develop DeepLasso, a deep learning model that can predict the RNAP inhibitory activity of an ubonodin variant.
Collapse
Affiliation(s)
- Alina Thokkadam
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Truc Do
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mark P. Brynildsen
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - A. James Link
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
18
|
Kim J, Lee SS, Fenter P, Myneni SCB, Nikitin V, Peters CA. Carbonate Coprecipitation for Cd and Zn Treatment and Evaluation of Heavy Metal Stability Under Acidic Conditions. Environ Sci Technol 2023; 57:3104-3113. [PMID: 36781166 PMCID: PMC9979612 DOI: 10.1021/acs.est.2c07678] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Mining wastes or combustion ash are materials of high carbon sequestration potential but are also known for their toxicity in terms of heavy metal content. To utilize such waste materials for engineered carbon mineralization purposes, there is a need to investigate the fate and mobility of toxic metals. This is a study of the coprecipitation of metals with calcium carbonate for environmental heavy metal mitigation. The study also examines the stability of precipitated phases under environmentally relevant acid conditions. For a wide range of cadmium (Cd) and zinc (Zn) concentrations (10 to 5000 mg/L), induced coprecipitation led to greater than 99% uptake from water. The calcium carbonate phases were found to contain amounts as high as 9.9 wt % (Cd) and 17 wt % (Zn), as determined by novel synchrotron techniques, including X-ray fluorescence element mapping and three-dimensional (3D) nanotransmission X-ray microscopy (TXM). TXM imaging revealed first-of-a-kind observations of chemical gradients and internal nanoporosity within particles. These observations provided new insights into the mechanisms leading to the retention of coprecipitated heavy metals during the dissolution of calcite in acidic (pH 4) solutions. These observations highlight the feasibility of utilizing carbonate coprecipitation as an engineered approach to the durable sequestration of toxic metals.
Collapse
Affiliation(s)
- Julie
J. Kim
- Department
of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Sang Soo Lee
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, United States
| | - Paul Fenter
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, United States
| | - Satish C. B. Myneni
- Department
of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Viktor Nikitin
- Advanced
Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Catherine A. Peters
- Department
of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
19
|
Xu X, Guillomaitre N, Christie KSS, Bay RK, Bizmark N, Datta SS, Ren ZJ, Priestley RD. Quick-Release Antifouling Hydrogels for Solar-Driven Water Purification. ACS Cent Sci 2023; 9:177-185. [PMID: 36844496 PMCID: PMC9951281 DOI: 10.1021/acscentsci.2c01245] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 06/18/2023]
Abstract
Hydrogels are promising soft materials for energy and environmental applications, including sustainable and off-grid water purification and harvesting. A current impediment to technology translation is the low water production rate well below daily human demand. To overcome this challenge, we designed a rapid-response, antifouling, loofah-inspired solar absorber gel (LSAG) capable of producing potable water from various contaminated sources at a rate of ∼26 kg m-2 h-1, which is sufficient to meet daily water demand. The LSAG-produced at room temperature via aqueous processing using an ethylene glycol (EG)-water mixture-uniquely integrates the attributes of poly(N-isopropylacrylamide) (PNIPAm), polydopamine (PDA), and poly(sulfobetaine methacrylate) (PSBMA) to enable off-grid water purification with enhanced photothermal response and the capacity to prevent oil fouling and biofouling. The use of the EG-water mixture was critical to forming the loofah-like structure with enhanced water transport. Remarkably, under sunlight irradiations of 1 and 0.5 sun, the LSAG required only 10 and 20 min to release ∼70% of its stored liquid water, respectively. Equally important, we demonstrate the ability of LSAG to purify water from various harmful sources, including those containing small molecules, oils, metals, and microplastics.
Collapse
Affiliation(s)
- Xiaohui Xu
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Néhémie Guillomaitre
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Kofi S. S. Christie
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - R. Ko̅nane Bay
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Navid Bizmark
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Sujit S. Datta
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Zhiyong Jason Ren
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| | - Rodney D. Priestley
- Department
of Chemical and Biological Engineering, Department of Mechanical and Aerospace
Engineering, Princeton Materials Institute, Department of Civil and Environmental Engineering, and Andlinger Center
for Energy and the Environment, Princeton
University, Princeton, New Jersey 08540, United States
| |
Collapse
|
20
|
Dongmo Wamba M, Montagner JP, Romanowicz B. Imaging deep-mantle plumbing beneath La Réunion and Comores hot spots: Vertical plume conduits and horizontal ponding zones. Sci Adv 2023; 9:eade3723. [PMID: 36696491 PMCID: PMC9876543 DOI: 10.1126/sciadv.ade3723] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Whether the two large low-shear velocity provinces (LLSVPs) at the base of Earth's mantle are wide compact structures extending thousands of kilometers upward or bundles of distinct mantle plumes is the subject of debate. Full waveform shear wave tomography of the deep mantle beneath the Indian Ocean highlights the presence of several separate broad low-velocity conduits anchored at the core-mantle boundary in the eastern part of the African LLSVP, most clearly beneath La Réunion and Comores hot spots. The deep plumbing system beneath these hot spots may also include alternating vertical conduits and horizontal ponding zones, from 1000-km depth to the top of the asthenosphere, reminiscent of dyke and sills in crustal volcanic systems, albeit at a whole-mantle scale.
Collapse
Affiliation(s)
- Mathurin Dongmo Wamba
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ 08544, USA
| | - Jean-Paul Montagner
- Université de Paris/Institut de Physique du Globe de Paris, UMR CNRS 7154, Paris, France
| | - Barbara Romanowicz
- Université de Paris/Institut de Physique du Globe de Paris, UMR CNRS 7154, Paris, France
- Collège de France, 11 Place Marcelin Berthelot, 75005 Paris, France
- Berkeley Seismological Laboratory, 291 McCone Hall, Berkeley, CA 94720, USA
| |
Collapse
|
21
|
Tien T, Saccomano SC, Martin PA, Armstrong MS, Prud’homme RK, Cash KJ. Sensors in a Flash! Oxygen Nanosensors for Microbial Metabolic Monitoring Synthesized by Flash Nanoprecipitation. ACS Sens 2022; 7:2606-2614. [PMID: 36053212 PMCID: PMC9513798 DOI: 10.1021/acssensors.2c00859] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/25/2022] [Indexed: 01/31/2023]
Abstract
Flash nanoprecipitation (FNP) is an efficient and scalable nanoparticle synthesis method that has not previously been applied to nanosensor fabrication. Current nanosensor fabrication methods have traditionally exhibited poor replicability and consistency resulting in high batch-to-batch variability, highlighting the need for a more tunable and efficient method such as FNP. We used FNP to fabricate nanosensors to sense oxygen based on an oxygen-sensitive dye and a reference dye, as a tool for measuring microbial metabolism. We used fluorescence spectroscopy to optimize nanosensor formulations, calibrate the nanosensors for oxygen concentration determination, and measure oxygen concentrations through oxygen-sensitive dye luminescence. FNP provides an effective platform for making sensors capable of responding to oxygen concentration in gas-bubbled solutions as well as in microbial environments. The environments we tested the sensors in arePseudomonas aeruginosa biofilms andSaccharomyces cerevisiae liquid cultures─both settings where oxygen concentration is highly dependent on microbial activity. With FNP now applied to nanosensor fabrication, future nanosensor applications can take advantage of improved product quality through better replicability and consistency while maintaining the original function of the nanosensor.
Collapse
Affiliation(s)
- Tony Tien
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Samuel C. Saccomano
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Pilar A. Martin
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Madeleine S. Armstrong
- Chemical
and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K. Prud’homme
- Chemical
and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Kevin J. Cash
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering, Colorado School
of Mines, Golden, Colorado 80401, United
States
| |
Collapse
|
22
|
Abstract
Behavioral constraints may explain part of the low demand for preventive health products. We test the effects of two light-touch psychological interventions on water chlorination and related health and economic outcomes using a randomized controlled trial among 3,750 women in rural Kenya. One intervention encourages participants to visualize alternative realizations of the future, and the other builds participants' ability to make concrete plans. After 12 weeks, visualization increases objectively measured chlorination, reduces diarrhea episodes among children, and increases savings. Effects on chlorination and savings persist after almost 3 years. Effects of the planning intervention are weaker and largely insignificant. Analysis of mechanisms suggests both interventions increase self-efficacy-beliefs about one's ability to achieve desired outcomes. Visualization also increases participants' skill in forecasting their future utility. The interventions do not differentially affect beliefs and knowledge about chlorination. Results suggest simple psychological interventions can increase future-oriented behaviors, including use of preventive health technologies.
Collapse
Affiliation(s)
- Anett John
- Department of Economics, University of Birmingham, UK
| | - Kate Orkin
- Blavatnik School of Government and Centre for Study of African Economies, University of Oxford, UK
| |
Collapse
|
23
|
LaChance J, Schottdorf M, Zajdel TJ, Saunders JL, Dvali S, Marshall C, Seirup L, Sammour I, Chatburn RL, Notterman DA, Cohen DJ. PVP1-The People's Ventilator Project: A fully open, low-cost, pressure-controlled ventilator research platform compatible with adult and pediatric uses. PLoS One 2022; 17:e0266810. [PMID: 35544461 PMCID: PMC9094548 DOI: 10.1371/journal.pone.0266810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/28/2022] [Indexed: 12/03/2022] Open
Abstract
Mechanical ventilators are safety-critical devices that help patients breathe, commonly found in hospital intensive care units (ICUs)-yet, the high costs and proprietary nature of commercial ventilators inhibit their use as an educational and research platform. We present a fully open ventilator device-The People's Ventilator: PVP1-with complete hardware and software documentation including detailed build instructions and a DIY cost of $1,700 USD. We validate PVP1 against both key performance criteria specified in the U.S. Food and Drug Administration's Emergency Use Authorization for Ventilators, and in a pediatric context against a state-of-the-art commercial ventilator. Notably, PVP1 performs well over a wide range of test conditions and performance stability is demonstrated for a minimum of 75,000 breath cycles over three days with an adult mechanical test lung. As an open project, PVP1 can enable future educational, academic, and clinical developments in the ventilator space.
Collapse
Affiliation(s)
- Julienne LaChance
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Manuel Schottdorf
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
| | - Tom J. Zajdel
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jonny L. Saunders
- Department of Psychology and Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Sophie Dvali
- Department of Physics, Princeton University, Princeton, New Jersey, United States of America
| | - Chase Marshall
- RailPod, Inc., Boston, Massachusetts, United States of America
| | - Lorenzo Seirup
- New York ISO, Rensselaer, New York, United States of America
| | - Ibrahim Sammour
- Department of Neonatology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, United States of America
| | - Robert L. Chatburn
- Department of Neonatology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, United States of America
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Daniel J. Cohen
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
24
|
Tong S, Singh NK, Sknepnek R, Košmrlj A. Linear viscoelastic properties of the vertex model for epithelial tissues. PLoS Comput Biol 2022; 18:e1010135. [PMID: 35587514 PMCID: PMC9159552 DOI: 10.1371/journal.pcbi.1010135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/01/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where constituent cells actively tune their mechanical properties to change the overall response of the tissue, e.g., from solid-like to fluid-like. Mesoscopic mechanical properties of epithelia are commonly modeled with the vertex model. While previous studies have predominantly focused on the rheological properties of the vertex model at long time scales, we systematically studied the full dynamic range by applying small oscillatory shear and bulk deformations in both solid-like and fluid-like phases for regular hexagonal and disordered cell configurations. We found that the shear and bulk responses in the fluid and solid phases can be described by standard spring-dashpot viscoelastic models. Furthermore, the solid-fluid transition can be tuned by applying pre-deformation to the system. Our study provides insights into the mechanisms by which epithelia can regulate their rich rheological behavior.
Collapse
Affiliation(s)
- Sijie Tong
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Navreeta K. Singh
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Rastko Sknepnek
- School of Science and Engineering, University of Dundee, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
- Princeton Institute of Materials, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
25
|
Wagnon GS, Pletcher OM, Brown CR. Change in beak overhangs of cliff swallows over 40 years: Partly a response to parasites? PLoS One 2022; 17:e0263422. [PMID: 35192650 PMCID: PMC8863248 DOI: 10.1371/journal.pone.0263422] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Some birds exhibit a maxillary overhang, in which the tip of the upper beak projects beyond the lower mandible and may curve downward. The overhang is thought to help control ectoparasites on the feathers. Little is known about the extent to which the maxillary overhang varies spatially or temporally within populations of the same species. The colonial cliff swallow (Petrochelidon pyrrhonota) has relatively recently shifted to almost exclusive use of artificial structures such as bridges and highway culverts for nesting and consequently has been exposed to higher levels of parasitism than on its ancestral cliff nesting sites. We examined whether increased ectoparasitism may have favored recent changes in the extent of the maxillary overhang. Using a specimen collection of cliff swallows from western Nebraska, USA, spanning 40 years and field data on live birds, we found that the extent of the maxillary overhang increased across years in a nonlinear way, peaking in the late 2000’s, and varied inversely with cliff swallow colony size for unknown reasons. The number of fleas on nestling cliff swallows declined in general over this period. Those birds with perceptible overhangs had fewer swallow bugs on the outside of their nest, but they did not have higher nesting success than birds with no overhangs. The intraspecific variation in the maxillary overhang in cliff swallows was partly consistent with it having a functional role in combatting ectoparasites. The temporal increase in the extent of the overhang may be a response by cliff swallows to their relatively recent increased exposure to parasitism. Our results demonstrate that this avian morphological trait can change rapidly over time.
Collapse
Affiliation(s)
- Gigi S. Wagnon
- Department of Biological Sciences, University of Tulsa, Tulsa, Oklahoma, United States of America
| | - Olivia M. Pletcher
- Department of Biological Sciences, University of Tulsa, Tulsa, Oklahoma, United States of America
| | - Charles R. Brown
- Department of Biological Sciences, University of Tulsa, Tulsa, Oklahoma, United States of America
- * E-mail:
| |
Collapse
|
26
|
Abstract
The brilliant iridescent plumage of birds creates some of the most stunning color displays known in the natural world. Iridescent plumage colors are produced by nanostructures in feathers and have evolved in diverse birds. The building blocks of these structures-melanosomes (melanin-filled organelles)-come in a variety of forms, yet how these different forms contribute to color production across birds remains unclear. Here, we leverage evolutionary analyses, optical simulations, and reflectance spectrophotometry to uncover general principles that govern the production of brilliant iridescence. We find that a key feature that unites all melanosome forms in brilliant iridescent structures is thin melanin layers. Birds have achieved this in multiple ways: by decreasing the size of the melanosome directly, by hollowing out the interior, or by flattening the melanosome into a platelet. The evolution of thin melanin layers unlocks color-producing possibilities, more than doubling the range of colors that can be produced with a thick melanin layer and simultaneously increasing brightness. We discuss the implications of these findings for the evolution of iridescent structures in birds and propose two evolutionary paths to brilliant iridescence.
Collapse
Affiliation(s)
- Klara Katarina Nordén
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Chad M Eliason
- Grainger Bioinformatics Center, Field Museum of Natural HistoryChicagoUnited States
| | - Mary Caswell Stoddard
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrincetonUnited States
| |
Collapse
|
27
|
Downie AE, Mayer A, Metcalf CJE, Graham AL. Optimal immune specificity at the intersection of host life history and parasite epidemiology. PLoS Comput Biol 2021; 17:e1009714. [PMID: 34932551 PMCID: PMC8730424 DOI: 10.1371/journal.pcbi.1009714] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/05/2022] [Accepted: 12/02/2021] [Indexed: 11/30/2022] Open
Abstract
Hosts diverge widely in how, and how well, they defend themselves against infection and immunopathology. Why are hosts so heterogeneous? Both epidemiology and life history are commonly hypothesized to influence host immune strategy, but the relationship between immune strategy and each factor has commonly been investigated in isolation. Here, we show that interactions between life history and epidemiology are crucial for determining optimal immune specificity and sensitivity. We propose a demographically-structured population dynamics model, in which we explore sensitivity and specificity of immune responses when epidemiological risks vary with age. We find that variation in life history traits associated with both reproduction and longevity alters optimal immune strategies-but the magnitude and sometimes even direction of these effects depends on how epidemiological risks vary across life. An especially compelling example that explains previously-puzzling empirical observations is that depending on whether infection risk declines or rises at reproductive maturity, later reproductive maturity can select for either greater or lower immune specificity, potentially illustrating why studies of lifespan and immune variation across taxa have been inconclusive. Thus, the sign of selection on the life history-immune specificity relationship can be reversed in different epidemiological contexts. Drawing on published life history data from a variety of chordate taxa, we generate testable predictions for this facet of the optimal immune strategy. Our results shed light on the causes of the heterogeneity found in immune defenses both within and among species and the ultimate variability of the relationship between life history and immune specificity.
Collapse
Affiliation(s)
- Alexander E. Downie
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Andreas Mayer
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - C. Jessica E. Metcalf
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
| | - Andrea L. Graham
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
28
|
Peck FC, Gabard-Durnam LJ, Wilkinson CL, Bosl W, Tager-Flusberg H, Nelson CA. Prediction of autism spectrum disorder diagnosis using nonlinear measures of language-related EEG at 6 and 12 months. J Neurodev Disord 2021; 13:57. [PMID: 34847887 PMCID: PMC8903497 DOI: 10.1186/s11689-021-09405-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early identification of autism spectrum disorder (ASD) provides an opportunity for early intervention and improved developmental outcomes. The use of electroencephalography (EEG) in infancy has shown promise in predicting later ASD diagnoses and in identifying neural mechanisms underlying the disorder. Given the high co-morbidity with language impairment, we and others have speculated that infants who are later diagnosed with ASD have altered language learning, including phoneme discrimination. Phoneme learning occurs rapidly in infancy, so altered neural substrates during the first year of life may serve as early, accurate indicators of later autism diagnosis. METHODS Using EEG data collected at two different ages during a passive phoneme task in infants with high familial risk for ASD, we compared the predictive accuracy of a combination of feature selection and machine learning models at 6 months (during native phoneme learning) and 12 months (after native phoneme learning), and we identified a single model with strong predictive accuracy (100%) for both ages. Samples at both ages were matched in size and diagnoses (n = 14 with later ASD; n = 40 without ASD). Features included a combination of power and nonlinear measures across the 10‑20 montage electrodes and 6 frequency bands. Predictive features at each age were compared both by feature characteristics and EEG scalp location. Additional prediction analyses were performed on all EEGs collected at 12 months; this larger sample included 67 HR infants (27 HR-ASD, 40 HR-noASD). RESULTS Using a combination of Pearson correlation feature selection and support vector machine classifier, 100% predictive diagnostic accuracy was observed at both 6 and 12 months. Predictive features differed between the models trained on 6- versus 12-month data. At 6 months, predictive features were biased to measures from central electrodes, power measures, and frequencies in the alpha range. At 12 months, predictive features were more distributed between power and nonlinear measures, and biased toward frequencies in the beta range. However, diagnosis prediction accuracy substantially decreased in the larger, more behaviorally heterogeneous 12-month sample. CONCLUSIONS These results demonstrate that speech processing EEG measures can facilitate earlier identification of ASD but emphasize the need for age-specific predictive models with large sample sizes to develop clinically relevant classification algorithms.
Collapse
Affiliation(s)
- Fleming C Peck
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Laurel J Gabard-Durnam
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Psychology, Northeastern University, Boston, MA, 02118, USA
| | - Carol L Wilkinson
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - William Bosl
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Health Informatics Program, University of San Francisco, San Francisco, CA, 94117, USA
| | - Helen Tager-Flusberg
- Department of Psychological and Brain Sciences, Boston University, Boston, MA, 02215, USA
| | - Charles A Nelson
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Graduate School of Education, Cambridge, MA, 02138, USA
| |
Collapse
|
29
|
Ding H, Chen Z, Wu K, Huang SM, Wu WL, LeBoeuf SE, Pillai RG, Rabinowitz JD, Papagiannakopoulos T. Activation of the NRF2 antioxidant program sensitizes tumors to G6PD inhibition. Sci Adv 2021; 7:eabk1023. [PMID: 34788087 PMCID: PMC8598006 DOI: 10.1126/sciadv.abk1023] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/27/2021] [Indexed: 05/20/2023]
Abstract
The KEAP1/NRF2 pathway promotes metabolic rewiring to support redox homeostasis. Activation of NRF2 occurs in many cancers, often due to KEAP1 mutations, and is associated with more aggressive disease and treatment resistance. To identify metabolic dependencies in cancers with NRF2 activation, we performed a metabolism-focused CRISPR screen. Glucose-6-phosphate dehydrogenase (G6PD), which was recently shown to be dispensable in Ras-driven tumors, was a top dependency. G6PD catalyzes the committed step of the oxidative pentose phosphate pathway that produces NADPH and nucleotide precursors, but neither antioxidants nor nucleosides rescued. Instead, G6PD loss triggered tricarboxylic acid (TCA) intermediate depletion because of up-regulation of the alternative NADPH-producing enzymes malic enzyme and isocitrate dehydrogenase. In vivo, G6PD impairment markedly suppressed KEAP1 mutant tumor growth, and this suppression was further augmented by TCA depletion by glutaminase inhibition. Thus, G6PD inhibition–induced TCA depletion is a therapeutic vulnerability of NRF2-activated cancer.
Collapse
Affiliation(s)
- Hongyu Ding
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Zihong Chen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, 91 Prospect Avenue, Princeton, NJ 08544, USA
| | - Katherine Wu
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Shih Ming Huang
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Warren L. Wu
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Sarah E. LeBoeuf
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Ray G. Pillai
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, VA New York Harbor Healthcare System, 423 East 23rd Avenue, New York, NY 10016, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, 91 Prospect Avenue, Princeton, NJ 08544, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
30
|
Chan ZT, Meunier S. Behind the screen: Understanding national support for a foreign investment screening mechanism in the European Union. Rev Int Organ 2021; 17:513-541. [PMID: 35719695 PMCID: PMC8275636 DOI: 10.1007/s11558-021-09436-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] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 06/15/2023]
Abstract
UNLABELLED What determines national preferences for institutionalizing foreign direct investment (FDI) screening? Over the past decade, advanced economies worldwide have tightened their national investment screening mechanisms (ISMs). In March 2019, the European Union (EU) adopted its first common FDI screening framework. This article explores variations in Member State preferences for the creation and nature of a pan-European screening framework. Based on extensive interviews with high-level EU and country officials involved in the negotiation process, and using a unique measure of national support for the EU-wide ISM created through the first-ever elite survey on this subject matter, we find that countries with higher technological levels were more supportive of FDI screening due to concerns over unreciprocated technological transfer. We also show the effects of Chinese FDI on country-level support for FDI screening sector-dependent. We found no evidence that total Chinese FDI predicts preferences for ISM. Instead, countries with high levels of Chinese FDI in strategic sectors are more likely to support the ISM, while those with high levels of Chinese investment in low-tech sectors tend to oppose screening. Our overall findings suggest that EU investment screening, and national-level screening in general, might become more restrictive in the future, especially in light of the COVID-19 pandemic. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11558-021-09436-y.
Collapse
Affiliation(s)
- Zenobia T. Chan
- Department of Politics, Princeton University, Fisher Hall, Princeton, NJ 08544-1012 USA
| | - Sophie Meunier
- School of Public and International Affairs, Princeton University, Roberson Hall, Princeton, NJ 08544-1013 USA
| |
Collapse
|
31
|
Abstract
OBJECTIVE Bacteria are exposed to multiple concurrent antimicrobial stressors within phagosomes. Among the antimicrobials produced, hydrogen peroxide and nitric oxide are two of the most deleterious products. In a previous study, we discovered that when faced with both stressors simultaneously, Escherichia coli prioritized detoxification of hydrogen peroxide over nitric oxide. In this study, we investigated whether such a process was conserved in another bacterium, Pseudomonas aeruginosa. RESULTS P. aeruginosa prioritized hydrogen peroxide detoxification in a dose-dependent manner. Specifically, hydrogen peroxide detoxification was unperturbed by the presence of nitric oxide, whereas larger doses of hydrogen peroxide produced longer delays in nitric oxide detoxification. Computational modelling revealed that the rate of nitric oxide consumption in co-treated cultures was biphasic, with cells entering the second phase of detoxification only after hydrogen peroxide was eliminated from the culture.
Collapse
Affiliation(s)
| | - Mark P. Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
| |
Collapse
|
32
|
Abstract
The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many antigens collectively shape the immune repertoire. Here, using mathematical modeling and statistical analyses of T cell receptor sequencing data, we develop a quantitative theory of human T cell dynamics compatible with the statistical laws of repertoire organization. We find that clonal expansions during a perinatal time window leave a long-lasting imprint on the human T cell repertoire, which is only slowly reshaped by fluctuating clonal selection during adult life. Our work provides a mechanism for how early clonal dynamics imprint the hierarchy of T cell clone sizes with implications for pathogen defense and autoimmunity.
Collapse
Affiliation(s)
- Mario U Gaimann
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität MünchenMünchenGermany
| | - Maximilian Nguyen
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
| | - Jonathan Desponds
- NSF-Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States
| | - Andreas Mayer
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
| |
Collapse
|
33
|
Mei S, Xu X, Priestley RD, Lu Y. Polydopamine-based nanoreactors: synthesis and applications in bioscience and energy materials. Chem Sci 2020; 11:12269-12281. [PMID: 34094435 PMCID: PMC8162453 DOI: 10.1039/d0sc04486e] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/21/2020] [Indexed: 11/21/2022] Open
Abstract
Polydopamine (PDA)-based nanoreactors have shown exceptional promise as multifunctional materials due to their nanoscale dimensions and sub-microliter volumes for reactions of different systems. Biocompatibility, abundance of active sites, and excellent photothermal conversion have facilitated their extensive use in bioscience and energy storage/conversion. This minireview summarizes recent advances in PDA-based nanoreactors, as applied to the abovementioned fields. We first highlight the design and synthesis of functional PDA-based nanoreactors with structural and compositional diversity. Special emphasis in bioscience has been given to drug/protein delivery, photothermal therapy, and antibacterial properties, while for energy-related applications, the focus is on electrochemical energy storage, catalysis, and solar energy harvesting. In addition, perspectives on pressing challenges and future research opportunities regarding PDA-based nanoreactors are discussed.
Collapse
Affiliation(s)
- Shilin Mei
- Department for Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie 14109 Berlin Germany
| | - Xiaohui Xu
- Department of Chemical and Biological Engineering, Princeton University New Jersey 08544 USA
| | - Rodney D Priestley
- Department of Chemical and Biological Engineering, Princeton University New Jersey 08544 USA
- Princeton Institute of the Science and Technology of Materials, Princeton University New Jersey 08544 USA
| | - Yan Lu
- Department for Electrochemical Energy Storage, Helmholtz-Zentrum Berlin für Materialien und Energie 14109 Berlin Germany
- Institute of Chemistry, University of Potsdam 14476 Potsdam Germany
| |
Collapse
|
34
|
Lea AJ, Martins D, Kamau J, Gurven M, Ayroles JF. Urbanization and market integration have strong, nonlinear effects on cardiometabolic health in the Turkana. Sci Adv 2020; 6:eabb1430. [PMID: 33087362 PMCID: PMC7577730 DOI: 10.1126/sciadv.abb1430] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/04/2020] [Indexed: 05/11/2023]
Abstract
The "mismatch" between evolved human physiology and Western lifestyles is thought to explain the current epidemic of cardiovascular disease (CVD) in industrialized societies. However, this hypothesis has been difficult to test because few populations concurrently span ancestral and modern lifestyles. To address this gap, we collected interview and biomarker data from individuals of Turkana ancestry who practice subsistence-level, nomadic pastoralism (the ancestral way of life for this group), as well as individuals who no longer practice pastoralism and live in urban areas. We found that Turkana who move to cities exhibit poor cardiometabolic health, partially because of a shift toward "Western diets" high in refined carbohydrates. We also show that being born in an urban area independently predicts adult health, such that life-long city dwellers will experience the greatest CVD risk. By focusing on a substantial lifestyle gradient, our work thus informs the timing, magnitude, and evolutionary causes of CVD.
Collapse
Affiliation(s)
- Amanda J Lea
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Dino Martins
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
- Mpala Research Centre, Nanyuki, Kenya
| | - Joseph Kamau
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Michael Gurven
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Julien F Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA.
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| |
Collapse
|
35
|
Martínez Cano I, Shevliakova E, Malyshev S, Wright SJ, Detto M, Pacala SW, Muller-Landau HC. Allometric constraints and competition enable the simulation of size structure and carbon fluxes in a dynamic vegetation model of tropical forests (LM3PPA-TV). Glob Chang Biol 2020; 26:4478-4494. [PMID: 32463934 DOI: 10.1111/gcb.15188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/31/2019] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Tropical forests are a key determinant of the functioning of the Earth system, but remain a major source of uncertainty in carbon cycle models and climate change projections. In this study, we present an updated land model (LM3PPA-TV) to improve the representation of tropical forest structure and dynamics in Earth system models (ESMs). The development and parameterization of LM3PPA-TV drew on extensive datasets on tropical tree traits and long-term field censuses from Barro Colorado Island (BCI), Panama. The model defines a new plant functional type (PFT) based on the characteristics of shade-tolerant, tropical tree species, implements a new growth allocation scheme based on realistic tree allometries, incorporates hydraulic constraints on biomass accumulation, and features a new compartment for tree branches and branch fall dynamics. Simulation experiments reproduced observed diurnal and seasonal patterns in stand-level carbon and water fluxes, as well as mean canopy and understory tree growth rates, tree size distributions, and stand-level biomass on BCI. Simulations at multiple sites captured considerable variation in biomass and size structure across the tropical forest biome, including observed responses to precipitation and temperature. Model experiments suggested a major role of water limitation in controlling geographic variation forest biomass and structure. However, the failure to simulate tropical forests under extreme conditions and the systematic underestimation of forest biomass in Paleotropical locations highlighted the need to incorporate variation in hydraulic traits and multiple PFTs that capture the distinct floristic composition across tropical domains. The continued pressure on tropical forests from global change demands models which are able to simulate alternative successional pathways and their pace to recovery. LM3PPA-TV provides a tool to investigate geographic variation in tropical forests and a benchmark to continue improving the representation of tropical forests dynamics and their carbon storage potential in ESMs.
Collapse
Affiliation(s)
- Isabel Martínez Cano
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Sergey Malyshev
- NOAA/Geophysical Fluid Dynamics Laboratory, Princeton, NJ, USA
| | | | - Matteo Detto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Stephen W Pacala
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | |
Collapse
|
36
|
Thawani A, Rale MJ, Coudray N, Bhabha G, Stone HA, Shaevitz JW, Petry S. The transition state and regulation of γ-TuRC-mediated microtubule nucleation revealed by single molecule microscopy. eLife 2020; 9:e54253. [PMID: 32538784 PMCID: PMC7338055 DOI: 10.7554/elife.54253] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 06/15/2020] [Indexed: 12/31/2022] Open
Abstract
Determining how microtubules (MTs) are nucleated is essential for understanding how the cytoskeleton assembles. While the MT nucleator, γ-tubulin ring complex (γ-TuRC) has been identified, precisely how γ-TuRC nucleates a MT remains poorly understood. Here, we developed a single molecule assay to directly visualize nucleation of a MT from purified Xenopus laevis γ-TuRC. We reveal a high γ-/αβ-tubulin affinity, which facilitates assembly of a MT from γ-TuRC. Whereas spontaneous nucleation requires assembly of 8 αβ-tubulins, nucleation from γ-TuRC occurs efficiently with a cooperativity of 4 αβ-tubulin dimers. This is distinct from pre-assembled MT seeds, where a single dimer is sufficient to initiate growth. A computational model predicts our kinetic measurements and reveals the rate-limiting transition where laterally associated αβ-tubulins drive γ-TuRC into a closed conformation. NME7, TPX2, and the putative activation domain of CDK5RAP2 h γ-TuRC-mediated nucleation, while XMAP215 drastically increases the nucleation efficiency by strengthening the longitudinal γ-/αβ-tubulin interaction.
Collapse
Affiliation(s)
- Akanksha Thawani
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Michael J Rale
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Nicolas Coudray
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Gira Bhabha
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton UniversityPrincetonUnited States
| | - Joshua W Shaevitz
- Lewis-Sigler Institute for Integrative GenomicsPrincetonUnited States
- Department of Physics, Princeton UniversityPrincetonUnited States
| | - Sabine Petry
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| |
Collapse
|
37
|
MacLennan SA, Eddy MP, Merschat AJ, Mehra AK, Crockford PW, Maloof AC, Southworth CS, Schoene B. Geologic evidence for an icehouse Earth before the Sturtian global glaciation. Sci Adv 2020; 6:eaay6647. [PMID: 32577504 PMCID: PMC7286673 DOI: 10.1126/sciadv.aay6647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Snowball Earth episodes, times when the planet was covered in ice, represent the most extreme climate events in Earth's history. Yet, the mechanisms that drive their initiation remain poorly constrained. Current climate models require a cool Earth to enter a Snowball state. However, existing geologic evidence suggests that Earth had a stable, warm, and ice-free climate before the Neoproterozoic Sturtian global glaciation [ca. 717 million years (Ma) ago]. Here, we present eruption ages for three felsic volcanic units interbedded with glaciolacustrine sedimentary rocks from southwest Virginia, USA, that demonstrate that glacially influenced sedimentation occurred at tropical latitudes ca. 751 Ma ago. Our findings are the first geologic evidence of a cool climate teetering on the edge of global glaciation several million years before the Sturtian Snowball Earth.
Collapse
Affiliation(s)
- Scott A. MacLennan
- Department of Geosciences, Princeton University, Princeton, NJ, USA
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY, USA
| | - Michael P. Eddy
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA
| | - Arthur J. Merschat
- Florence Bascom Geoscience Center, United States Geological Survey, MS926A, Reston, VA, USA
| | - Akshay K. Mehra
- Department of Geosciences, Princeton University, Princeton, NJ, USA
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
| | - Peter W. Crockford
- Department of Geosciences, Princeton University, Princeton, NJ, USA
- Weizmann Institute of Science, Rehovot, Israel
| | - Adam C. Maloof
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - C. Scott Southworth
- Florence Bascom Geoscience Center, United States Geological Survey, MS926A, Reston, VA, USA
| | - Blair Schoene
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| |
Collapse
|
38
|
Duprey NN, Wang TX, Kim T, Cybulski JD, Vonhof HB, Crutzen PJ, Haug GH, Sigman DM, Martínez-García A, Baker DM. Megacity development and the demise of coastal coral communities: Evidence from coral skeleton δ 15 N records in the Pearl River estuary. Glob Chang Biol 2020; 26:1338-1353. [PMID: 31732999 DOI: 10.1111/gcb.14923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/30/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Historical coral skeleton (CS) δ18 O and δ15 N records were produced from samples recovered from sedimentary deposits, held in natural history museum collections, and cored into modern coral heads. These records were used to assess the influence of global warming and regional eutrophication, respectively, on the decline of coastal coral communities following the development of the Pearl River Delta (PRD) megacity, China. We find that, until 2007, ocean warming was not a major threat to coral communities in the Pearl River estuary; instead, nitrogen (N) inputs dominated impacts. The high but stable CS-δ15 N values (9‰-12‰ vs. air) observed from the mid-Holocene until 1980 indicate that soil and stream denitrification reduced and modulated the hydrologic inputs of N, blunting the rise in coastal N sources during the early phase of the Pearl River estuary urbanization. However, an unprecedented CS-δ15 N peak was observed from 1987 to 1993 (>13‰ vs. air), concomitant to an increase of NH4+ concentration, consistent with the rapid Pearl River estuary urbanization as the main cause for this eutrophication event. We suggest that widespread discharge of domestic sewage entered directly into the estuary, preventing removal by natural denitrification hotspots. We argue that this event caused the dramatic decline of the Pearl River estuary coral communities reported from 1980 to 2000. Subsequently, the coral record shows that the implementation of improved wastewater management policies succeeded in bringing down both CS-δ15 N and NH4+ concentrations in the early 2000s. This study points to the potential importance of eutrophication over ocean warming in coral decline along urbanized coastlines and in particular in the vicinity of megacities.
Collapse
Affiliation(s)
- Nicolas N Duprey
- Max Planck Institute for Chemistry, Otto Hahn Institute, Mainz, Germany
- The Swire Institute of Marine Science, The University of Hong Kong, Shek O, HKSAR
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, HKSAR
| | - Tony X Wang
- Department of Geosciences, Princeton University, Princeton, NJ, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, MA, USA
| | - Taihun Kim
- The Swire Institute of Marine Science, The University of Hong Kong, Shek O, HKSAR
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, HKSAR
| | - Jonathan D Cybulski
- The Swire Institute of Marine Science, The University of Hong Kong, Shek O, HKSAR
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, HKSAR
| | - Hubert B Vonhof
- Max Planck Institute for Chemistry, Otto Hahn Institute, Mainz, Germany
| | - Paul J Crutzen
- Max Planck Institute for Chemistry, Otto Hahn Institute, Mainz, Germany
| | - Gerald H Haug
- Max Planck Institute for Chemistry, Otto Hahn Institute, Mainz, Germany
| | - Daniel M Sigman
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - David M Baker
- The Swire Institute of Marine Science, The University of Hong Kong, Shek O, HKSAR
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, HKSAR
| |
Collapse
|
39
|
Zipple MN, Archie EA, Tung J, Altmann J, Alberts SC. Intergenerational effects of early adversity on survival in wild baboons. eLife 2019; 8:e47433. [PMID: 31549964 PMCID: PMC6759315 DOI: 10.7554/elife.47433] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023] Open
Abstract
Early life adversity can affect an individual's health, survival, and fertility for many years after the adverse experience. Whether early life adversity also imposes intergenerational effects on the exposed individual's offspring is not well understood. We fill this gap by leveraging prospective, longitudinal data on a wild, long-lived primate. We find that juveniles whose mothers experienced early life adversity exhibit high mortality before age 4, independent of the juvenile's own experience of early adversity. These juveniles often preceded their mothers in death by 1 to 2 years, indicating that high adversity females decline in their ability to raise offspring near the end of life. While we cannot exclude direct effects of a parent's environment on offspring quality (e.g., inherited epigenetic changes), our results are completely consistent with a classic parental effect, in which the environment experienced by a parent affects its future phenotype and therefore its offspring's phenotype.
Collapse
Affiliation(s)
| | - Elizabeth A Archie
- Department of Biological SciencesUniversity of Notre DameSouth BendUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
| | - Jenny Tung
- Department of BiologyDuke UniversityDurhamUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Department of Evolutionary AnthropologyDuke UniversityDurhamUnited States
- Duke Population Research InstituteDuke UniversityDurhamUnited States
| | - Jeanne Altmann
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonUnited States
| | - Susan C Alberts
- Department of BiologyDuke UniversityDurhamUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Department of Evolutionary AnthropologyDuke UniversityDurhamUnited States
- Duke Population Research InstituteDuke UniversityDurhamUnited States
| |
Collapse
|
40
|
Saitta ET, Liang R, Lau MCY, Brown CM, Longrich NR, Kaye TG, Novak BJ, Salzberg SL, Norell MA, Abbott GD, Dickinson MR, Vinther J, Bull ID, Brooker RA, Martin P, Donohoe P, Knowles TDJ, Penkman KEH, Onstott T. Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities. eLife 2019; 8:e46205. [PMID: 31210129 PMCID: PMC6581507 DOI: 10.7554/elife.46205] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/12/2019] [Indexed: 12/12/2022] Open
Abstract
Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.
Collapse
Affiliation(s)
- Evan T Saitta
- Integrative Research Center, Section of Earth SciencesField Museum of Natural HistoryChicagoUnited States
| | - Renxing Liang
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
| | - Maggie CY Lau
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
- Institute of Deep-Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Caleb M Brown
- Royal Tyrrell Museum of PalaeontologyDrumhellerCanada
| | - Nicholas R Longrich
- Department of Biology and BiochemistryUniversity of BathBathUnited Kingdom
- Milner Centre for EvolutionUniversity of BathBathUnited Kingdom
| | - Thomas G Kaye
- Foundation for Scientific AdvancementSierra VistaUnited States
| | - Ben J Novak
- Revive and RestoreSan FranciscoUnited States
| | - Steven L Salzberg
- Department of Biomedical Engineering, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
- Department of Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
| | - Mark A Norell
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkUnited States
| | - Geoffrey D Abbott
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Jakob Vinther
- School of Earth SciencesUniversity of BristolBristolUnited Kingdom
- School of Biological SciencesUniversity of BristolBristolUnited Kingdom
| | - Ian D Bull
- School of ChemistryUniversity of BristolBristolUnited Kingdom
| | | | - Peter Martin
- School of PhysicsUniversity of BristolBristolUnited Kingdom
| | - Paul Donohoe
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Timothy DJ Knowles
- School of ChemistryUniversity of BristolBristolUnited Kingdom
- School of ArtsUniversity of BristolBristolUnited Kingdom
| | | | - Tullis Onstott
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
| |
Collapse
|
41
|
Liu M, Sharma AK, Shaevitz JW, Leifer AM. Temporal processing and context dependency in Caenorhabditis elegans response to mechanosensation. eLife 2018; 7:e36419. [PMID: 29943731 PMCID: PMC6054533 DOI: 10.7554/elife.36419] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/10/2018] [Indexed: 11/13/2022] Open
Abstract
A quantitative understanding of how sensory signals are transformed into motor outputs places useful constraints on brain function and helps to reveal the brain's underlying computations. We investigate how the nematode Caenorhabditis elegans responds to time-varying mechanosensory signals using a high-throughput optogenetic assay and automated behavior quantification. We find that the behavioral response is tuned to temporal properties of mechanosensory signals, such as their integral and derivative, that extend over many seconds. Mechanosensory signals, even in the same neurons, can be tailored to elicit different behavioral responses. Moreover, we find that the animal's response also depends on its behavioral context. Most dramatically, the animal ignores all tested mechanosensory stimuli during turns. Finally, we present a linear-nonlinear model that predicts the animal's behavioral response to stimulus.
Collapse
Affiliation(s)
- Mochi Liu
- Lewis-Sigler Institute for Integrative GenomicsPrinceton UniversityNew JerseyUnited States
| | - Anuj K Sharma
- Department of PhysicsPrinceton UniversityNew JerseyUnited States
| | - Joshua W Shaevitz
- Lewis-Sigler Institute for Integrative GenomicsPrinceton UniversityNew JerseyUnited States
- Department of PhysicsPrinceton UniversityNew JerseyUnited States
| | - Andrew M Leifer
- Department of PhysicsPrinceton UniversityNew JerseyUnited States
- Princeton Neuroscience InstitutePrinceton UniversityNew JerseyUnited States
| |
Collapse
|
42
|
Nguyen JP, Linder AN, Plummer GS, Shaevitz JW, Leifer AM. Automatically tracking neurons in a moving and deforming brain. PLoS Comput Biol 2017; 13:e1005517. [PMID: 28545068 PMCID: PMC5436637 DOI: 10.1371/journal.pcbi.1005517] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/11/2017] [Indexed: 11/18/2022] Open
Abstract
Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must be tracked in 3D over time to accurately extract single neuron activity traces. Recordings from small invertebrates like C. elegans are especially challenging because they undergo very large brain motion and deformation during animal movement. Here we present an automated computer vision pipeline to reliably track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. 3D volumetric fluorescent images of the animal's brain are straightened, aligned and registered, and the locations of neurons in the images are found via segmentation. Each neuron is then assigned an identity using a new time-independent machine-learning approach we call Neuron Registration Vector Encoding. In this approach, non-rigid point-set registration is used to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. The way each neuron matches with the references defines a feature vector which is clustered to assign an identity to each neuron in each volume. Finally, thin-plate spline interpolation is used to correct errors in segmentation and check consistency of assigned identities. The Neuron Registration Vector Encoding approach proposed here is uniquely well suited for tracking neurons in brains undergoing large deformations. When applied to whole-brain calcium imaging recordings in freely moving C. elegans, this analysis pipeline located 156 neurons for the duration of an 8 minute recording and consistently found more neurons more quickly than manual or semi-automated approaches.
Collapse
Affiliation(s)
- Jeffrey P. Nguyen
- Department of Physics, Princeton University, Princeton, New Jersey, United States of America
| | - Ashley N. Linder
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
| | - George S. Plummer
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Joshua W. Shaevitz
- Department of Physics, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Andrew M. Leifer
- Department of Physics, Princeton University, Princeton, New Jersey, United States of America
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
| |
Collapse
|
43
|
Davison EN, Turner BO, Schlesinger KJ, Miller MB, Grafton ST, Bassett DS, Carlson JM. Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan. PLoS Comput Biol 2016; 12:e1005178. [PMID: 27880785 PMCID: PMC5120784 DOI: 10.1371/journal.pcbi.1005178] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/03/2016] [Indexed: 11/18/2022] Open
Abstract
Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task") consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory"), in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.
Collapse
Affiliation(s)
- Elizabeth N. Davison
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Benjamin O. Turner
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Kimberly J. Schlesinger
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Michael B. Miller
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Scott T. Grafton
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Danielle S. Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jean M. Carlson
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| |
Collapse
|