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Sheta AM, Fernández S, Liu C, Dubed-Bandomo GC, Lloret-Fillol J. An Electrocatalytic Cascade Reaction for the Synthesis of Ketones Using CO 2 as a CO Surrogate. Angew Chem Int Ed Engl 2024:e202403674. [PMID: 38647344 DOI: 10.1002/anie.202403674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Indexed: 04/25/2024]
Abstract
The construction of carbonyl compounds via carbonylation reactions using safe CO sources remains a long-standing challenge to synthetic chemists. Herein, we propose a catalyst cascade Scheme in which CO2 is used as a CO surrogate in the carbonylation of benzyl chlorides. Our approach is based on the cooperation between two coexisting catalytic cycles: the CO2-to-CO electroreduction cycle promoted by [Fe(TPP)Cl] (TPP=meso-tetraphenylporphyrin) and an electrochemical carbonylation cycle catalyzed by [Ni(bpy)Br2] (2,2'-bipyridine). As a proof of concept, this protocol allows for the synthesis of symmetric ketones from good to excellent yields in an undivided cell with non-sacrificial electrodes. The reaction can be directly scaled up to gram-scale and operates effectively at a CO2 concentration of 10 %, demonstrating its robustness. Our mechanistic studies based on cyclic voltammetry, IR spectroelectrochemistry and Density Functional Theory calculations suggest a synergistic effect between the two catalysts. The CO produced from CO2 reduction is key in the formation of the [Ni(bpy)(CO)2], which is proposed as the catalytic intermediate responsible for the C-C bond formation in the carbonylation steps.
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Affiliation(s)
- Ahmed M Sheta
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Avda. Països Catalans, 16, 43007, Tarragona, Spain
- Departament de Química Orgànica i Analítica, Universitat Rovira i Virgili, Carrer Marcel ⋅ lí Domingo s/n, 43007, Tarragona, Spain
- Department of Chemistry, Damietta University, Damietta El-Gadeeda City, Kafr Saad, Damietta Governorate, 34511, Egypt
| | - Sergio Fernández
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Avda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Changwei Liu
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Avda. Països Catalans, 16, 43007, Tarragona, Spain
- Departament de Química Orgànica i Analítica, Universitat Rovira i Virgili, Carrer Marcel ⋅ lí Domingo s/n, 43007, Tarragona, Spain
| | - Geyla C Dubed-Bandomo
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Avda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Julio Lloret-Fillol
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Avda. Països Catalans, 16, 43007, Tarragona, Spain
- Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
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Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024. [PMID: 38451841 DOI: 10.1111/febs.17112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
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Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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Delgado S, Somovilla P, Ferrer-Orta C, Martínez-González B, Vázquez-Monteagudo S, Muñoz-Flores J, Soria ME, García-Crespo C, de Ávila AI, Durán-Pastor A, Gadea I, López-Galíndez C, Moran F, Lorenzo-Redondo R, Verdaguer N, Perales C, Domingo E. Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps. Proc Natl Acad Sci U S A 2024; 121:e2317851121. [PMID: 38416684 DOI: 10.1073/pnas.2317851121] [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: 10/16/2023] [Accepted: 01/08/2024] [Indexed: 03/01/2024] Open
Abstract
Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.
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Affiliation(s)
- Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos, Universidad Politécnica de Madrid, Madrid 28031, Spain
| | - Pilar Somovilla
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Ferrer-Orta
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Sergi Vázquez-Monteagudo
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | | | - María Eugenia Soria
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Carlos García-Crespo
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Ana Isabel de Ávila
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en retrovirus, Centro Nacional de Microbiología, Instituto de salud Carlos III, Majadahonda 28222, Spain
| | - Federico Moran
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611
| | - Nuria Verdaguer
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Esteban Domingo
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
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Yáñez-Gómez F, Gálvez-Melero L, Ledesma-Corvi S, Bis-Humbert C, Hernández-Hernández E, Salort G, García-Cabrerizo R, García-Fuster MJ. Evaluating the daily modulation of FADD and related molecular markers in different brain regions in male rats. J Neurosci Res 2024; 102:e25296. [PMID: 38361411 DOI: 10.1002/jnr.25296] [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] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 02/17/2024]
Abstract
Fas-Associated protein with Death Domain (FADD), a key molecule controlling cell fate by balancing apoptotic versus non-apoptotic functions, is dysregulated in post-mortem brains of subjects with psychopathologies, in animal models capturing certain aspects of these disorders, and by several pharmacological agents. Since persistent disruptions in normal functioning of daily rhythms are linked with these conditions, oscillations over time of key biomarkers, such as FADD, could play a crucial role in balancing the clinical outcome. Therefore, we characterized the 24-h regulation of FADD (and linked molecular partners: p-ERK/t-ERK ratio, Cdk-5, p35/p25, cell proliferation) in key brain regions for FADD regulation (prefrontal cortex, striatum, hippocampus). Samples were collected during Zeitgeber time (ZT) 2, ZT5, ZT8, ZT11, ZT14, ZT17, ZT20, and ZT23 (ZT0, lights-on or inactive period; ZT12, lights-off or active period). FADD showed similar daily fluctuations in all regions analyzed, with higher values during lights off, and opposite to p-ERK/t-ERK ratios regulation. Both Cdk-5 and p35 remained stable and did not change across ZT. However, p25 increased during lights off, but exclusively in striatum. Finally, no 24-h modulation was observed for hippocampal cell proliferation, although higher values were present during lights off. These results demonstrated a clear daily modulation of FADD in several key brain regions, with a more prominent regulation during the active time of rats, and suggested a key role for FADD, and molecular partners, in the normal physiological functioning of the brain's daily rhythmicity, which if disrupted might participate in the development of certain pathologies.
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Affiliation(s)
- Fernando Yáñez-Gómez
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Medicine, University of the Balearic Islands, Palma, Spain
| | - Laura Gálvez-Melero
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Sandra Ledesma-Corvi
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Cristian Bis-Humbert
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Elena Hernández-Hernández
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Glòria Salort
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Rubén García-Cabrerizo
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Medicine, University of the Balearic Islands, Palma, Spain
| | - M Julia García-Fuster
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Medicine, University of the Balearic Islands, Palma, Spain
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Manubens-Gil L, Pons-Espinal M, Gener T, Ballesteros-Yañez I, de Lagrán MM, Dierssen M. Deficits in neuronal architecture but not over-inhibition are main determinants of reduced neuronal network activity in a mouse model of overexpression of Dyrk1A. Cereb Cortex 2024; 34:bhad431. [PMID: 37997361 PMCID: PMC10793573 DOI: 10.1093/cercor/bhad431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/25/2023] Open
Abstract
In this study, we investigated the impact of Dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) overexpression, a gene associated with Down syndrome, on hippocampal neuronal deficits in mice. Our findings revealed that mice overexpressing Dyrk1A (TgDyrk1A; TG) exhibited impaired hippocampal recognition memory, disrupted excitation-inhibition balance, and deficits in long-term potentiation (LTP). Specifically, we observed layer-specific deficits in dendritic arborization of TG CA1 pyramidal neurons in the stratum radiatum. Through computational modeling, we determined that these alterations resulted in reduced storage capacity and compromised integration of inputs, with decreased high γ oscillations. Contrary to prevailing assumptions, our model suggests that deficits in neuronal architecture, rather than over-inhibition, primarily contribute to the reduced network. We explored the potential of environmental enrichment (EE) as a therapeutic intervention and found that it normalized the excitation-inhibition balance, restored LTP, and improved short-term recognition memory. Interestingly, we observed transient significant dendritic remodeling, leading to recovered high γ. However, these effects were not sustained after EE discontinuation. Based on our findings, we conclude that Dyrk1A overexpression-induced layer-specific neuromorphological disturbances impair the encoding of place and temporal context. These findings contribute to our understanding of the underlying mechanisms of Dyrk1A-related hippocampal deficits and highlight the challenges associated with long-term therapeutic interventions for cognitive impairments.
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Affiliation(s)
- Linus Manubens-Gil
- Institute for Brain Science and Intelligent Technology, Southeast University (SEU), Biomedical engineering, Sipailou street No. 2, Xuanwu district, 210096, Nanjing, China
- School of Biological Science and Medical Engineering, Southeast University (SEU), Sipailou street No. 2, Xuanwu district, 210096, Nanjing, China
| | - Meritxell Pons-Espinal
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, Avinguda de la Granvia de l'Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Avda. Diagonal, 643 Edifici Prevosti, planta -108028, Barcelona, Spain
| | - Thomas Gener
- Advanced Electronic Materials and Devices Group (AEMD), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, UAB Campus, Bellaterra Barcelona 08193, Spain
| | - Inmaculada Ballesteros-Yañez
- Inorganic and Organic Chemistry and Biochemistry, Faculty of Medicine, University of Castilla- La Mancha, Camino de Moledores, 13071, Ciudad Real, Spain
| | - María Martínez de Lagrán
- Cellular and Systems Neurobiology, Systems and Synthetic Biology Program, Center for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Mara Dierssen
- Cellular and Systems Neurobiology, Systems and Synthetic Biology Program, Center for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain
- Center for Biomedical Research in the Network of Rare Diseases (CIBERER), v. Monforte de Lemos, 3-5. Pabellón 11. Planta 0 28029, Madrid, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
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Lou XY, Yohai L, Boada R, Resina-Gallego M, Han D, Valiente M. Effective Removal of Boron from Aqueous Solutions by Inorganic Adsorbents: A Review. Molecules 2023; 29:59. [PMID: 38202645 PMCID: PMC10780067 DOI: 10.3390/molecules29010059] [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: 11/15/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Increasing levels of boron in water exceeding acceptable thresholds have triggered concerns regarding environmental pollution and adverse health effects. In response, significant efforts are being made to develop new adsorbents for the removal of boron from contaminated water. Among the various materials proposed, inorganic adsorbents have emerged as promising materials due to their chemical, thermal, and mechanical stability. This review aims to comprehensively examine recent advances made in the development of inorganic adsorbents for the efficient removal of boron from water. Firstly, the adsorption performance of the most used adsorbents, such as magnesium, iron, aluminum, and individual and mixed oxides, are summarized. Subsequently, diverse functionalization methods aimed at enhancing boron adsorption capacity and selectivity are carefully analyzed. Lastly, challenges and future perspectives in this field are highlighted to guide the development of innovative high-performance adsorbents and adsorption systems, ultimately leading to a reduction in boron pollution.
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Affiliation(s)
- Xiang-Yang Lou
- Grup de Tècniques de Separació en Química (GTS-UAB Research Group), Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (X.-Y.L.); (L.Y.); (M.R.-G.); (D.H.); (M.V.)
| | - Lucia Yohai
- Grup de Tècniques de Separació en Química (GTS-UAB Research Group), Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (X.-Y.L.); (L.Y.); (M.R.-G.); (D.H.); (M.V.)
- Instituto de Investigaciones en Ciencia y Tecnología de Materiales (INTEMA), Universidad Nacional de Mar del Plata-Consejo Nacional de Investigaciones Científicas y Técnicas (UNMdP-CONICET), Mar del Plata B7608FDQ, Argentina
| | - Roberto Boada
- Grup de Tècniques de Separació en Química (GTS-UAB Research Group), Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (X.-Y.L.); (L.Y.); (M.R.-G.); (D.H.); (M.V.)
| | - Montserrat Resina-Gallego
- Grup de Tècniques de Separació en Química (GTS-UAB Research Group), Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (X.-Y.L.); (L.Y.); (M.R.-G.); (D.H.); (M.V.)
| | - Dong Han
- Grup de Tècniques de Separació en Química (GTS-UAB Research Group), Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (X.-Y.L.); (L.Y.); (M.R.-G.); (D.H.); (M.V.)
| | - Manuel Valiente
- Grup de Tècniques de Separació en Química (GTS-UAB Research Group), Department of Chemistry, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (X.-Y.L.); (L.Y.); (M.R.-G.); (D.H.); (M.V.)
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7
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Blázquez-Encinas R, García-Vioque V, Caro-Cuenca T, Moreno-Montilla MT, Mangili F, Alors-Pérez E, Ventura S, Herrera-Martínez AD, Moreno-Casado P, Calzado MA, Salvatierra Á, Gálvez-Moreno MA, Fernandez-Cuesta L, Foll M, Luque RM, Alcala N, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery. J Transl Med 2023; 21:879. [PMID: 38049848 PMCID: PMC10696873 DOI: 10.1186/s12967-023-04754-8] [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: 05/05/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Lung neuroendocrine neoplasms (LungNENs) comprise a heterogeneous group of tumors ranging from indolent lesions with good prognosis to highly aggressive cancers. Carcinoids are the rarest LungNENs, display low to intermediate malignancy and may be surgically managed, but show resistance to radiotherapy/chemotherapy in case of metastasis. Molecular profiling is providing new information to understand lung carcinoids, but its clinical value is still limited. Altered alternative splicing is emerging as a novel cancer hallmark unveiling a highly informative layer. METHODS We primarily examined the status of the splicing machinery in lung carcinoids, by assessing the expression profile of the core spliceosome components and selected splicing factors in a cohort of 25 carcinoids using a microfluidic array. Results were validated in an external set of 51 samples. Dysregulation of splicing variants was further explored in silico in a separate set of 18 atypical carcinoids. Selected altered factors were tested by immunohistochemistry, their associations with clinical features were assessed and their putative functional roles were evaluated in vitro in two lung carcinoid-derived cell lines. RESULTS The expression profile of the splicing machinery was profoundly dysregulated. Clustering and classification analyses highlighted five splicing factors: NOVA1, SRSF1, SRSF10, SRSF9 and PRPF8. Anatomopathological analysis showed protein differences in the presence of NOVA1, PRPF8 and SRSF10 in tumor versus non-tumor tissue. Expression levels of each of these factors were differentially related to distinct number and profiles of splicing events, and were associated to both common and disparate functional pathways. Accordingly, modulating the expression of NOVA1, PRPF8 and SRSF10 in vitro predictably influenced cell proliferation and colony formation, supporting their functional relevance and potential as actionable targets. CONCLUSIONS These results provide primary evidence for dysregulation of the splicing machinery in lung carcinoids and suggest a plausible functional role and therapeutic targetability of NOVA1, PRPF8 and SRSF10.
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Affiliation(s)
- Ricardo Blázquez-Encinas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Víctor García-Vioque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Teresa Caro-Cuenca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Pathology Service, Reina Sofía University Hospital, Córdoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Federica Mangili
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Emilia Alors-Pérez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Sebastian Ventura
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Aura D Herrera-Martínez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Paula Moreno-Casado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - Marco A Calzado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Ángel Salvatierra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - María A Gálvez-Moreno
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Lynnette Fernandez-Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Raúl M Luque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Sergio Pedraza-Arevalo
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain.
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8
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Roman-Juan J, Solé E, Sánchez-Rodríguez E, Castarlenas E, Jensen MP, Miró J. Adverse Childhood Events and Chronic Pain in Adolescents: The Role of Sleep Disturbance. J Pediatr Psychol 2023; 48:931-939. [PMID: 37743052 DOI: 10.1093/jpepsy/jsad063] [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: 05/22/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
OBJECTIVES This study aimed to (1) examine the extent to which the association between exposure to adverse childhood events (ACEs) and having chronic pain in adolescents is explained by the association between exposure to ACEs and sleep disturbance and (2) explore the role of sleep disturbance in the association between exposure to ACEs and anxiety and depressive symptoms in adolescents with chronic pain. METHODS Cross-sectional data from 469 adolescents aged 13-18 years old were drawn from an epidemiological study on pediatric chronic pain conducted in Catalonia (Spain). Participants provided self-reports of demographic characteristics, exposure to ACEs, pain characteristics, sleep disturbance, anxiety, and depressive symptoms. Mediation and moderation models were conducted. RESULTS Sleep disturbance explained a significant amount of the variance in the association between exposure to ACEs and the presence of chronic pain. Moreover, sleep disturbance explained a significant amount of the variance in the association between exposure to ACEs and depressive symptoms and moderated the association between exposure to ACEs and anxiety in adolescents with chronic pain. CONCLUSION The study findings suggest the possibility that addressing sleep disturbance in adolescents exposed to ACEs may help to prevent the development of chronic pain, anxiety, and depressive symptoms in those adolescents who already have chronic pain.
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Affiliation(s)
- Josep Roman-Juan
- Universitat Rovira i Virgili, Spain
- Department of Psychology, Unit for the Study and Treatment of Pain-ALGOS, Research Center for Behavior Assessment (CRAMC), Spain
| | - Ester Solé
- Universitat Rovira i Virgili, Spain
- Department of Psychology, Unit for the Study and Treatment of Pain-ALGOS, Research Center for Behavior Assessment (CRAMC), Spain
| | - Elisabet Sánchez-Rodríguez
- Universitat Rovira i Virgili, Spain
- Department of Psychology, Unit for the Study and Treatment of Pain-ALGOS, Research Center for Behavior Assessment (CRAMC), Spain
| | - Elena Castarlenas
- Universitat Rovira i Virgili, Spain
- Department of Psychology, Unit for the Study and Treatment of Pain-ALGOS, Research Center for Behavior Assessment (CRAMC), Spain
| | - Mark P Jensen
- Department of Rehabilitation Medicine, University of Washington, USA
| | - Jordi Miró
- Universitat Rovira i Virgili, Spain
- Department of Psychology, Unit for the Study and Treatment of Pain-ALGOS, Research Center for Behavior Assessment (CRAMC), Spain
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9
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Lamparelli DH, Villar-Yanez A, Dittrich L, Rintjema J, Bravo F, Bo C, Kleij AW. Bicyclic Guanidine Promoted Mechanistically Divergent Depolymerization and Recycling of a Biobased Polycarbonate. Angew Chem Int Ed Engl 2023:e202314659. [PMID: 37934031 DOI: 10.1002/anie.202314659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
We here report the organocatalytic and temperature-controlled depolymerization of biobased poly(limonene carbonate) providing access to its trans-configured cyclic carbonate as the major product. The base TBD (1,5,7-triazabicyclo[4.4.0]dec-5-ene) offers a unique opportunity to break down polycarbonates via end-group activation or main chain scission pathways as supported by various controls and computational analysis. These energetically competitive processes represent an unprecedented divergent approach to polycarbonate recycling. The trans limonene carbonate can be converted back to its polycarbonate via ring-opening polymerization using the same organocatalyst in the presence of an alcohol initiator, offering thus a potential circular and practical route for polycarbonate recycling.
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Affiliation(s)
- David H Lamparelli
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Alba Villar-Yanez
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
- Departament de Química Física i Inorgànica/, Universitat Rovira i Virgili, Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - Lorenz Dittrich
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Jeroen Rintjema
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Fernando Bravo
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
- Departament de Química Física i Inorgànica/, Universitat Rovira i Virgili, Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - Arjan W Kleij
- Institute of Chemical Research of Catalonia (ICIQ-Cerca), the Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
- Catalan Institute of Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
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10
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Thompson PJ, Pipella J, Rutter GA, Gaisano HY, Santamaria P. Islet autoimmunity in human type 1 diabetes: initiation and progression from the perspective of the beta cell. Diabetologia 2023; 66:1971-1982. [PMID: 37488322 PMCID: PMC10542715 DOI: 10.1007/s00125-023-05970-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 07/26/2023]
Abstract
Type 1 diabetes results from the poorly understood process of islet autoimmunity, which ultimately leads to the loss of functional pancreatic beta cells. Mounting evidence supports the notion that the activation and evolution of islet autoimmunity in genetically susceptible people is contingent upon early life exposures affecting the islets, especially beta cells. Here, we review some of the recent advances and studies that highlight the roles of these changes as well as antigen presentation and stress response pathways in beta cells in the onset and propagation of the autoimmune process in type 1 diabetes. Future progress in this area holds promise for advancing islet- and beta cell-directed therapies that could be implemented in the early stages of the disease and could be combined with immunotherapies.
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Affiliation(s)
- Peter J Thompson
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
- Department of Physiology & Pathophysiology, University of Manitoba, Winnipeg, MB, Canada.
| | - Jasmine Pipella
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Physiology & Pathophysiology, University of Manitoba, Winnipeg, MB, Canada
| | - Guy A Rutter
- CRCHUM and Department of Medicine, Université de Montréal, Montréal, QC, Canada.
- Department of Diabetes, Endocrinology and Medicine, Faculty of Medicine, Imperial College, London, UK.
- LKC School of Medicine, Nanyang Technological College, Singapore, Republic of Singapore.
| | - Herbert Y Gaisano
- Departments of Medicine and Physiology, University of Toronto, Toronto, ON, Canada
| | - Pere Santamaria
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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11
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Machuca-Márquez P, Sánchez-Benito L, Menardy F, Urpi A, Girona M, Puighermanal E, Appiah I, Palmiter RD, Sanz E, Quintana A. Vestibular CCK signaling drives motion sickness-like behavior in mice. Proc Natl Acad Sci U S A 2023; 120:e2304933120. [PMID: 37847729 PMCID: PMC10622874 DOI: 10.1073/pnas.2304933120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/23/2023] [Indexed: 10/19/2023] Open
Abstract
Travel can induce motion sickness (MS) in susceptible individuals. MS is an evolutionary conserved mechanism caused by mismatches between motion-related sensory information and past visual and motion memory, triggering a malaise accompanied by hypolocomotion, hypothermia, hypophagia, and nausea. Vestibular nuclei (VN) are critical for the processing of movement input from the inner ear. Motion-induced activation of VN neurons recapitulates MS-related signs. However, the genetic identity of VN neurons mediating MS-related autonomic and aversive responses remains unknown. Here, we identify a central role of cholecystokinin (CCK)-expressing VN neurons in motion-induced malaise. Moreover, we show that CCK VN inputs onto the parabrachial nucleus activate Calca-expressing neurons and are sufficient to establish avoidance to novel food, which is prevented by CCK-A receptor antagonism. These observations provide greater insight into the neurobiological regulation of MS by identifying the neural substrates of MS and providing potential targets for treatment.
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Affiliation(s)
| | - Laura Sánchez-Benito
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Fabien Menardy
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Andrea Urpi
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Mònica Girona
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Emma Puighermanal
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Isabella Appiah
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Richard D. Palmiter
- HHMI, University of Washington, Seattle, WA98195
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Elisenda Sanz
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona08193, Spain
| | - Albert Quintana
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona08193, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona08193, Spain
- Focus Area for Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom2520, South Africa
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12
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Thoenen L, Giroud C, Kreuzer M, Waelchli J, Gfeller V, Deslandes-Hérold G, Mateo P, Robert CAM, Ahrens CH, Rubio-Somoza I, Bruggmann R, Erb M, Schlaeppi K. Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome. Proc Natl Acad Sci U S A 2023; 120:e2310134120. [PMID: 37878725 PMCID: PMC10622871 DOI: 10.1073/pnas.2310134120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
Plants exude specialized metabolites from their roots, and these compounds are known to structure the root microbiome. However, the underlying mechanisms are poorly understood. We established a representative collection of maize root bacteria and tested their tolerance against benzoxazinoids (BXs), the dominant specialized and bioactive metabolites in the root exudates of maize plants. In vitro experiments revealed that BXs inhibited bacterial growth in a strain- and compound-dependent manner. Tolerance against these selective antimicrobial compounds depended on bacterial cell wall structure. Further, we found that native root bacteria isolated from maize tolerated the BXs better compared to nonhost Arabidopsis bacteria. This finding suggests the adaptation of the root bacteria to the specialized metabolites of their host plant. Bacterial tolerance to 6-methoxy-benzoxazolin-2-one (MBOA), the most abundant and selective antimicrobial metabolite in the maize rhizosphere, correlated significantly with the abundance of these bacteria on BX-exuding maize roots. Thus, strain-dependent tolerance to BXs largely explained the abundance pattern of bacteria on maize roots. Abundant bacteria generally tolerated MBOA, while low abundant root microbiome members were sensitive to this compound. Our findings reveal that tolerance to plant specialized metabolites is an important competence determinant for root colonization. We propose that bacterial tolerance to root-derived antimicrobial compounds is an underlying mechanism determining the structure of host-specific microbial communities.
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Affiliation(s)
- Lisa Thoenen
- Institute of Plant Sciences, University of Bern, Bern3013, Switzerland
- Department of Environmental Sciences, University of Basel, Basel4056, Switzerland
| | - Caitlin Giroud
- Department of Environmental Sciences, University of Basel, Basel4056, Switzerland
| | - Marco Kreuzer
- Interfaculty Bioinformatics Unit, University of Bern, Bern3012, Switzerland
| | - Jan Waelchli
- Department of Environmental Sciences, University of Basel, Basel4056, Switzerland
| | - Valentin Gfeller
- Institute of Plant Sciences, University of Bern, Bern3013, Switzerland
| | | | - Pierre Mateo
- Institute of Plant Sciences, University of Bern, Bern3013, Switzerland
| | | | - Christian H. Ahrens
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich8046, Switzerland
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution Lab, Centre for Research in Agricultural Genomics, Barcelona08193, Spain
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Bern3012, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern3013, Switzerland
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern3013, Switzerland
- Department of Environmental Sciences, University of Basel, Basel4056, Switzerland
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13
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Kaci K, Enebral-Romero E, Martínez-Periñán E, Garrido M, Pérez EM, López-Diego D, Luna M, González-de-Rivera G, García-Mendiola T, Lorenzo E. Multiplex Portable Biosensor for Bacteria Detection. Biosensors (Basel) 2023; 13:958. [PMID: 37998133 PMCID: PMC10669278 DOI: 10.3390/bios13110958] [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: 09/11/2023] [Revised: 10/11/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
An advanced, cost-effective, and portable DNA biosensor capable of detecting multiple bacteria simultaneously has been developed. The biosensor comprises a fast and inexpensive potentiostat that controls the applied potential to a screen-printed electrochemical array platform functionalized with MoS2 flakes and bacterial DNA probes. The current response obtained by à la carte thionine functionalized carbon nanodots (Ty-CDs) is monitored as an electrochemical indicator of the hybridization event. The design of the potentiostat prioritizes achieving an optimal signal-to-noise ratio and incorporates a user-friendly interface compatible with various devices, including computers, mobile phones, and tablets. The device is compact, lightweight, and manufactured at a low cost. The key components of the potentiostat include a data acquisition board capable of analyzing multiple samples simultaneously and a controller board. The results of this study confirm the ability of the multiplex portable biosensor to successfully detect specific bacterial DNA sequences, demonstrating its reliability and superior performance compared with a traditional, more complex, and laboratory-oriented potentiostat.
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Affiliation(s)
- Karim Kaci
- HCTLab, Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (K.K.); (G.G.-d.-R.)
| | - Estefanía Enebral-Romero
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.E.-R.); (E.M.-P.); (E.L.)
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain; (M.G.); (E.M.P.)
| | - Emiliano Martínez-Periñán
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.E.-R.); (E.M.-P.); (E.L.)
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Marina Garrido
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain; (M.G.); (E.M.P.)
| | - Emilio M. Pérez
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain; (M.G.); (E.M.P.)
| | - David López-Diego
- Instituto de Micro y Nanotecnología IMN-CNM, CSIC (CEI UAM+CSIC), 28760 Madrid, Spain; (D.L.-D.); (M.L.)
| | - Mónica Luna
- Instituto de Micro y Nanotecnología IMN-CNM, CSIC (CEI UAM+CSIC), 28760 Madrid, Spain; (D.L.-D.); (M.L.)
| | | | - Tania García-Mendiola
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.E.-R.); (E.M.-P.); (E.L.)
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Encarnación Lorenzo
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (E.E.-R.); (E.M.-P.); (E.L.)
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain; (M.G.); (E.M.P.)
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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14
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Montes-Garrido R, Anel-Lopez L, Riesco MF, Neila-Montero M, Palacin-Martinez C, Soriano-Úbeda C, Boixo JC, de Paz P, Anel L, Alvarez M. Does Size Matter? Testicular Volume and Its Predictive Ability of Sperm Production in Rams. Animals (Basel) 2023; 13:3204. [PMID: 37893928 PMCID: PMC10603633 DOI: 10.3390/ani13203204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Over the years, testicular volume has been used to evaluate the reproductive capacity of rams and the effects of different factors related to reproductive performance. The aim of this study was to determine the most suitable tool and formula to calculate testicular volume under field conditions to guarantee a more accurate determination of sperm production. First, testicles from 25 rams (n = 50) were measured in vivo and postmortem using calipers and ultrasonography during the breeding season (BS). The accurate testicular volume (ATV) was calculated through water displacement. In addition, the sexual status of donor rams was evaluated during a period of four years in a reproduction center, and the three most crucial groups in terms of genetic value and seminal collections were studied in the second part of this experiment: ER-NBS (Elite rams during the non-breeding season), ER-BS-S (Elite rams with a standard frequency of seminal collection), and ER-BS-O (Elite rams with a high frequency of seminal collection). The total testicular volume (TTV), testosterone (T), and total spermatozoa obtained from two consecutive ejaculates in the same day (SPERM) were measured, and the relationship between SPERM and TTV and T was analyzed to predict SPERM. Although all published formulas revealed statistically significant differences (p ≤ 0.05) from the ATV, our proposed formula (ItraULE) (Testicular volume = L × W × D × 0.61) did not show significant differences. In the second part of the study, in the ER as a model donor ram for its high genetic value and high demand from farmers, TTV and T showed strong positive correlations with SPERM (r = 0.587, p = 0.007 NBS; r = 0.684, p = 0.001 BS-S; r = 0.773, p < 0.0001 BS-O). Moreover, formulas were established to predict SPERM in these practical scenarios. In conclusion, the use of ultrasonography and a new formula adapted to rams could improve the prediction of SPERM considering crucial factors such as season and semen collection frequency.
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Affiliation(s)
- Rafael Montes-Garrido
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
| | - Luis Anel-Lopez
- ITRAULE, Anatomy, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain
| | - Marta F. Riesco
- ITRAULE, Cellular Biology, Department of Molecular Biology, University of León, 24071 León, Spain; (M.F.R.); (P.d.P.)
| | - Marta Neila-Montero
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
| | - Cristina Palacin-Martinez
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
| | - Cristina Soriano-Úbeda
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
| | - Juan Carlos Boixo
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
| | - Paulino de Paz
- ITRAULE, Cellular Biology, Department of Molecular Biology, University of León, 24071 León, Spain; (M.F.R.); (P.d.P.)
| | - Luis Anel
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
| | - Mercedes Alvarez
- ITRAULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery, and Anatomy, University of León, 24071 León, Spain; (R.M.-G.); (M.N.-M.); (C.P.-M.); (C.S.-Ú.); (J.C.B.); (L.A.); (M.A.)
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15
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Oltolina F, Santaella Escolano MDC, Jabalera Y, Prat M, Jimenez Lopez C. mAb-Functionalized Biomimetic MamC-Mediated-Magnetoliposomes as Drug Delivery Systems for Cancer Therapy. Int J Mol Sci 2023; 24:13958. [PMID: 37762260 PMCID: PMC10531091 DOI: 10.3390/ijms241813958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
In cancer therapy, new therapeutic nanoformulations able to mediate targeted chemotherapy are required. Recently, biomimetic magnetic nanoparticles (BMNPs) mediated by MamC, a magnetosome protein from Magnetococcus marinus MC-1, have proven, in vitro and in vivo, to be effective drug nanocarriers (following the application of an external gradient magnetic field) and to allow combination with hyperthermia. However, these nanoassemblies require further optimization to improve cytocompatibility, stability and active targeting ability. Herein, we describe the production of the magnetoliposomes (LP) embedding BMNPs functionalized (or not) with doxorubicin (DOXO), [LP(+/-DOXO-BMNPs)], and their surface modification with the DO-24 mAb, which targets the human Met/HGF receptor's ectodomain (overexpressed in many cancers). Nanoformulations were extensively characterized using TEM, DLS, FTIR and when tested in vitro, the lipid coating increased the colloidal stability and their biocompatibility, favoring the cellular uptake in cells overexpressing the cognate receptor. Indeed, the magnetoliposomes mAb-LP(+/-DOXO-BMNPs) exerted a specific active targeting ability by the presence of the mAb that preserved its immunocompetence. Both LP(BMNPs) and mAb-LP(BMNPs) were not toxic to cells, while +/-mAb-LP(DOXO-BMNPs) nanoformulations were indeed cytotoxic. Therefore, this study represents a proof of concept for the development of promising drug carriers for cancer therapy based on local chemotherapy directed by mAbs.
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Affiliation(s)
- Francesca Oltolina
- Department of Microbiology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (M.d.C.S.E.); (Y.J.); (C.J.L.)
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale “A. Avogadro”, Via Solaroli 17, 28100 Novara, Italy;
| | | | - Ylenia Jabalera
- Department of Microbiology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (M.d.C.S.E.); (Y.J.); (C.J.L.)
| | - Maria Prat
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale “A. Avogadro”, Via Solaroli 17, 28100 Novara, Italy;
| | - Concepcion Jimenez Lopez
- Department of Microbiology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (M.d.C.S.E.); (Y.J.); (C.J.L.)
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16
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Gil-Rivas A, de Pascual-Teresa B, Ortín I, Ramos A. New Advances in the Exploration of Esterases with PET and Fluorescent Probes. Molecules 2023; 28:6265. [PMID: 37687094 PMCID: PMC10488407 DOI: 10.3390/molecules28176265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Esterases are hydrolases that catalyze the hydrolysis of esters into the corresponding acids and alcohols. The development of fluorescent probes for detecting esterases is of great importance due to their wide spectrum of biological and industrial applications. These probes can provide a rapid and sensitive method for detecting the presence and activity of esterases in various samples, including biological fluids, food products, and environmental samples. Fluorescent probes can also be used for monitoring the effects of drugs and environmental toxins on esterase activity, as well as to study the functions and mechanisms of these enzymes in several biological systems. Additionally, fluorescent probes can be designed to selectively target specific types of esterases, such as those found in pathogenic bacteria or cancer cells. In this review, we summarize the recent fluorescent probes described for the visualization of cell viability and some applications for in vivo imaging. On the other hand, positron emission tomography (PET) is a nuclear-based molecular imaging modality of great value for studying the activity of enzymes in vivo. We provide some examples of PET probes for imaging acetylcholinesterases and butyrylcholinesterases in the brain, which are valuable tools for diagnosing dementia and monitoring the effects of anticholinergic drugs on the central nervous system.
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Affiliation(s)
- Alba Gil-Rivas
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
| | - Irene Ortín
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
| | - Ana Ramos
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
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17
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Álvarez-Rodríguez L, Ríos P, Laglera-Gándara CJ, Jurado A, Fernández-de-Córdova FJ, Gunnoe TB, Rodríguez A. Cleavage of Carbon Dioxide C=O Bond Promoted by Nickel-Boron Cooperativity in a PBP-Ni Complex. Angew Chem Int Ed Engl 2023; 62:e202306315. [PMID: 37399341 DOI: 10.1002/anie.202306315] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
The synthesis and characterization of (tBu PBP)Ni(OAc) (5) by insertion of carbon dioxide into the Ni-C bond of (tBu PBP)NiMe (1) is presented. An unexpected CO2 cleavage process involving the formation of new B-O and Ni-CO bonds leads to the generation of a butterfly-structured tetra-nickel cluster (tBu PBOP)2 Ni4 (μ-CO)2 (6). Mechanistic investigation of this reaction indicates a reductive scission of CO2 by O-atom transfer to the boron atom via a cooperative nickel-boron mechanism. The CO2 activation reaction produces a three-coordinate (tBu P2 BO)Ni-acyl intermediate (A) that leads to a (tBu P2 BO)-NiI complex (B) via a likely radical pathway. The NiI species is trapped by treatment with the radical trap (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) to give (tBu P2 BO)NiII (η2 -TEMPO) (7). Additionally, 13 C and 1 H NMR spectroscopy analysis using 13 C-enriched CO2 provides information about the species involved in the CO2 activation process.
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Affiliation(s)
- Lucía Álvarez-Rodríguez
- Instituto de Investigaciones Químicas-Departamento de Química Inorgánica, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Américo Vespucio 49, 41092, Sevilla, Spain
| | - Pablo Ríos
- Instituto de Investigaciones Químicas-Departamento de Química Inorgánica, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Américo Vespucio 49, 41092, Sevilla, Spain
| | - Carlos J Laglera-Gándara
- Instituto de Investigaciones Químicas-Departamento de Química Inorgánica, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Américo Vespucio 49, 41092, Sevilla, Spain
| | - Andrea Jurado
- Instituto de Investigaciones Químicas-Departamento de Química Inorgánica, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Américo Vespucio 49, 41092, Sevilla, Spain
| | - Francisco José Fernández-de-Córdova
- Instituto de Investigaciones Químicas-Departamento de Química Inorgánica, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Américo Vespucio 49, 41092, Sevilla, Spain
| | - T Brent Gunnoe
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Amor Rodríguez
- Instituto de Investigaciones Químicas-Departamento de Química Inorgánica, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Américo Vespucio 49, 41092, Sevilla, Spain
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18
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Gámez-Valenzuela S, Torres-Moya I, Sánchez A, Donoso B, López Navarrete JT, Ruiz Delgado MC, Prieto P, Ponce Ortiz R. Extended π-Conjugation and Structural Planarity Effects of Symmetrical D-π-A-π-D Naphthalene and Perylene Diimide Semiconductors on n-type Electrical Properties. Chemistry 2023; 29:e202301639. [PMID: 37265227 DOI: 10.1002/chem.202301639] [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: 05/23/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/03/2023]
Abstract
A series of donor-π-acceptor-π-donor (D-π-A-π-D) compounds based on naphthalendiimide (NDI) and perylenediimide (PDI) central cores combined with triphenylamine and phenylcarbazole donor groups have been synthesized, characterized and tested in top-contact/bottom gate organic field-effect transistors (OFETs). The results showed high electron mobilities, up to 0.3 cm2 V-1 s-1 , in the case of NDI derivatives and moderate values of around 10-3 cm2 V-1 s-1 for PDI-based semiconductors. Quantum chemical calculations were performed in order to support the experimental data. The results suggest that adequate molecular characteristics and larger crystalline domains in NDI vs. PDI semiconducting films may be the reasons behind the enhanced electrical properties of NDI derivatives. Furthermore, when the lateral donor substituents are triphenylamine groups, the mobilities were slightly higher in comparison to phenylcarbazole donor groups due to an improved electron-donating character. Other characterization techniques, such as AFM, X-ray diffraction or spectroelectrochemistry, among others, have been performed to analyze supramolecular order, charge carriers' nature and stability, parameters closely related to charge transport characteristics.
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Affiliation(s)
- Sergio Gámez-Valenzuela
- Department of Physical Chemistry, University of Malaga Campus de Teatinos s/n, Malaga, 29071, Spain
| | - Iván Torres-Moya
- Department of Inorganic, Organic Chemistry and Biochemistry University of Castilla-La Mancha-IRICA, Faculty of Science and Chemical Technologies, Ciudad Real, 13071, Spain
- Department of Organic Chemistry, University of Murcia Campus of Espinardo, Murcia, 30005, Spain
| | - Abelardo Sánchez
- Department of Inorganic, Organic Chemistry and Biochemistry University of Castilla-La Mancha-IRICA, Faculty of Science and Chemical Technologies, Ciudad Real, 13071, Spain
| | - Beatriz Donoso
- Department of Inorganic, Organic Chemistry and Biochemistry University of Castilla-La Mancha-IRICA, Faculty of Science and Chemical Technologies, Ciudad Real, 13071, Spain
| | | | - M Carmen Ruiz Delgado
- Department of Physical Chemistry, University of Malaga Campus de Teatinos s/n, Malaga, 29071, Spain
| | - Pilar Prieto
- Department of Inorganic, Organic Chemistry and Biochemistry University of Castilla-La Mancha-IRICA, Faculty of Science and Chemical Technologies, Ciudad Real, 13071, Spain
| | - Rocío Ponce Ortiz
- Department of Physical Chemistry, University of Malaga Campus de Teatinos s/n, Malaga, 29071, Spain
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19
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Rasti G, Becker M, Vazquez BN, Espinosa-Alcantud M, Fernández-Duran I, Gámez-García A, Ianni A, Gonzalez J, Bosch-Presegué L, Marazuela-Duque A, Guitart-Solanes A, Segura-Bayona S, Bech-Serra JJ, Scher M, Serrano L, Shankavaram U, Erdjument-Bromage H, Tempst P, Reinberg D, Olivella M, Stracker T, de la Torre C, Vaquero A. SIRT1 regulates DNA damage signaling through the PP4 phosphatase complex. Nucleic Acids Res 2023; 51:6754-6769. [PMID: 37309898 PMCID: PMC10359614 DOI: 10.1093/nar/gkad504] [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: 09/22/2022] [Revised: 05/24/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023] Open
Abstract
The Sirtuin family of NAD+-dependent enzymes plays an important role in maintaining genome stability upon stress. Several mammalian Sirtuins have been linked directly or indirectly to the regulation of DNA damage during replication through Homologous recombination (HR). The role of one of them, SIRT1, is intriguing as it seems to have a general regulatory role in the DNA damage response (DDR) that has not yet been addressed. SIRT1-deficient cells show impaired DDR reflected in a decrease in repair capacity, increased genome instability and decreased levels of γH2AX. Here we unveil a close functional antagonism between SIRT1 and the PP4 phosphatase multiprotein complex in the regulation of the DDR. Upon DNA damage, SIRT1 interacts specifically with the catalytical subunit PP4c and promotes its inhibition by deacetylating the WH1 domain of the regulatory subunits PP4R3α/β. This in turn regulates γH2AX and RPA2 phosphorylation, two key events in the signaling of DNA damage and repair by HR. We propose a mechanism whereby during stress, SIRT1 signaling ensures a global control of DNA damage signaling through PP4.
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Affiliation(s)
- George Rasti
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Maximilian Becker
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Berta N Vazquez
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Maria Espinosa-Alcantud
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Irene Fernández-Duran
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
| | - Andrés Gámez-García
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
| | - Alessandro Ianni
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231Bad Nauheim, Germany
| | - Jessica Gonzalez
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Bosch-Presegué
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
- Tissue Repair and Regeneration Laboratory (TR2Lab), Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IrisCC). Experimental Sciences and Methodology Department. Faculty of Health Sciences and Welfare (FCSB), University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Anna Marazuela-Duque
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Guitart-Solanes
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
| | - Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Current affiliation: The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Joan-Josep Bech-Serra
- Proteomic Unit, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Barcelona, Spain
| | - Michael Scher
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, NJ08854, USA
| | - Lourdes Serrano
- Department of Science, BMCC, The City University of New York (CUNY), 199 Chambers Street N699P, New Yirk, NY10007, USA
| | - Uma Shankavaram
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD20892, USA
| | - Hediye Erdjument-Bromage
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY10065, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY10016, USA
| | - Paul Tempst
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY10065, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, NJ08854, USA
- Howard Hughes Medical Institute, Department of Biochemistry, New York University School of Medicine, New York, NY10016, USA
| | - Mireia Olivella
- Bioinfomatics and Medical Statistics Group, Faculty of Science, Technology and Engineering. University of Vic-Central University of Catalonia, Vic, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD20892, USA
| | - Carolina de la Torre
- Proteomic Unit, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Barcelona, Spain
| | - Alejandro Vaquero
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain
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20
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Redondo-Gómez S, Mesa-Marín J, Pérez-Romero JA, Mariscal V, Molina-Heredia FP, Álvarez C, Pajuelo E, Rodríguez-Llorente ID, Mateos-Naranjo E. Plant Growth-Promoting Rhizobacteria Improve Rice Response to Climate Change Conditions. Plants (Basel) 2023; 12:2532. [PMID: 37447093 DOI: 10.3390/plants12132532] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/20/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023]
Abstract
Rice is one of the most important crops in the world and is considered a strategic crop for food security. Furthermore, the excessive use of chemical fertilizers to obtain high yields causes environmental problems. A sustainable alternative includes taking advantage of beneficial bacteria that promote plant growth. Here, we investigate the effect of five bacterial biofertilizers from halophytes on growth, and we investigate photosynthetic efficiency in rice plants grown under saline conditions (0 and 85 mmol L-1 NaCl) and future climate change scenarios, including increased CO2 concentrations and temperature (400/700 ppm and 25/+4 °C, respectively). Biofertilizers 1-4 increased growth by 9-64% in plants grown with and without salt in both CO2- temperature combinations, although there was no significant positive effect on the net photosynthetic rate of rice plants. In general, biofertilizer 1 was the most effective at 400 ppm CO2 and at 700 ppm CO2 +4 °C in the absence of salt. Inocula 1-5 also stimulated plant length at high CO2 levels without salt. Finally, the positive effect of biofertilization was attenuated in the plants grown under the interaction between salt and high CO2. This highlights the significance of studying biofertilization under stress interaction to establish the real potential of biofertilizers in the context of climate change conditions.
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Affiliation(s)
- Susana Redondo-Gómez
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Jennifer Mesa-Marín
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Jesús A Pérez-Romero
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, 11510 Puerto Real, Spain
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, 41092 Seville, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, 41092 Seville, Spain
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, 41092 Seville, Spain
| | - Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012 Seville, Spain
| | - Ignacio D Rodríguez-Llorente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012 Seville, Spain
| | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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21
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Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M. Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Res 2023; 51:5864-5882. [PMID: 37207342 PMCID: PMC10287934 DOI: 10.1093/nar/gkad397] [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: 07/19/2022] [Revised: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.
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Affiliation(s)
- Aleix Tarrés-Solé
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Joachim M Gerhold
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Olivier Piétrement
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | | | - Elena Ruiz-López
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Inserm, CNRS and Université de Montpellier, France, Sébastien Lyonnais, UAR 3725 CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Joaquim Roca
- Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Maria Solà
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
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22
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Pascari X, Weigel S, Marin S, Sanchis V, Maul R. Detection and quantification of zearalenone and its modified forms in enzymatically treated oat and wheat flour. J Food Sci Technol 2023; 60:1367-1375. [PMID: 36936126 PMCID: PMC10020390 DOI: 10.1007/s13197-023-05683-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/04/2022] [Accepted: 01/29/2023] [Indexed: 02/19/2023]
Abstract
An analytical method for the analysis of the mycotoxin zearalenone (ZEN) and its modified forms was developed. Sample preparation was performed based on a modified QuEChERS method combined with liquid chromatography coupled to a triple quadrupole mass spectrometry detection. The method was tested for linearity, precision, limits of detection and quantification and recoveries. The evaluation of the above-mentioned parameters was performed on oat flour. The method was applied to oat and wheat flours that were submitted to an amylolytic treatment (α-amylase and amyloglucosidase), similar to the one used in the cereal-based baby food production process. A decrease in β-zearalenol (β-ZEL) and β-ZEL-14-sulfate of approximately 40% after 90 min incubation was observed, the other analytes did not show any significant changes. To our knowledge, this is the first method that approaches the identification and assessment of ZEN-sulfate derivates in a cereal matrix. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05683-6.
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Affiliation(s)
- Xenia Pascari
- grid.15043.330000 0001 2163 1432Applied Mycology Unit, Food Technology Department, University of Lleida, UTPV-XaRTA, Agrotecnio, Av. Rovira Roure 191, 25198 Lleida, Spain
| | - Stefan Weigel
- grid.417830.90000 0000 8852 3623Department Safety in the Food Chain, BfR German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Sonia Marin
- grid.15043.330000 0001 2163 1432Applied Mycology Unit, Food Technology Department, University of Lleida, UTPV-XaRTA, Agrotecnio, Av. Rovira Roure 191, 25198 Lleida, Spain
| | - Vicente Sanchis
- grid.15043.330000 0001 2163 1432Applied Mycology Unit, Food Technology Department, University of Lleida, UTPV-XaRTA, Agrotecnio, Av. Rovira Roure 191, 25198 Lleida, Spain
| | - Ronald Maul
- grid.417830.90000 0000 8852 3623Department Safety in the Food Chain, BfR German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
- grid.72925.3b0000 0001 1017 8329Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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23
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Amo L, Amo de Paz G, Kabbert J, Machordom A. House sparrows do not exhibit a preference for the scent of potential partners with different MHC-I diversity and genetic distances. PLoS One 2022; 17:e0278892. [PMID: 36542616 PMCID: PMC9770374 DOI: 10.1371/journal.pone.0278892] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
MHC genes play a fundamental role in immune recognition of pathogens and parasites. Therefore, females may increase offspring heterozygosity and genetic diversity by selecting males with genetically compatible or heterozygous MHC. In birds, several studies suggest that MHC genes play a role in mate choice, and recent evidence suggests that olfaction may play a role in the MHC-II discrimination. However, whether olfaction is involved in MHC-I discrimination in birds remains unknown. Previous studies indicate that house sparrow females with low allelic diversity prefer males with higher diversity in MHC-I alleles. Here, we directly explored whether female and male house sparrows (Passer domesticus) could estimate by scent MHC-I diversity and/or dissimilarity of potential partners. Our results show that neither females nor males exhibit a preference related to MHC-I diversity or dissimilarity of potential partners, suggesting that MHC-I is not detected through olfaction. Further studies are needed to understand the mechanisms responsible for mate discrimination based on MHC-I in birds.
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Affiliation(s)
- Luisa Amo
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Móstoles, Spain
- * E-mail:
| | - Guillermo Amo de Paz
- Departamento de Farmacología, Farmacognosia y Botánica, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Johanna Kabbert
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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24
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Pagnamenta AT, Diaz-Gonzalez F, Banos-Pinero B, Ferla MP, Toosi MB, Calder AD, Karimiani EG, Doosti M, Wainwright A, Wordsworth P, Bailey K, Ejeskär K, Lester T, Maroofian R, Heath KE, Tajsharghi H, Shears D, Taylor JC. Variable skeletal phenotypes associated with biallelic variants in PRKG2. J Med Genet 2022; 59:947-950. [PMID: 34782440 PMCID: PMC9554069 DOI: 10.1136/jmedgenet-2021-108027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/08/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Alistair T Pagnamenta
- NIHR Biomedical Research Centre, Oxford, Oxfordshire, UK
- Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, UK
| | - Francisca Diaz-Gonzalez
- INGEMM, IdiPAZ and Skeletal Dysplasia Multidisciplinary Unit (UMDE, ERN-BOND), Hospital Universitario La Paz, Madrid, Spain
| | - Benito Banos-Pinero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Matteo P Ferla
- NIHR Biomedical Research Centre, Oxford, Oxfordshire, UK
- Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, UK
| | - Mehran B Toosi
- Department of Pediatric Neurology, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alistair D Calder
- Radiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ehsan G Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's, University of London, London, UK
- Next Generation Genetic Polyclinic, Razavi International Hospital, Mashhad, Iran
| | - Mohammad Doosti
- Next Generation Genetic Polyclinic, Razavi International Hospital, Mashhad, Iran
| | - Andrew Wainwright
- Department of Paediatrics, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Wordsworth
- NIHR Biomedical Research Centre, Oxford, Oxfordshire, UK
- Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, UK
- Department of Paediatrics, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kathryn Bailey
- Department of Paediatrics, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Katarina Ejeskär
- School of Health Sciences, Translational Medicine, University of Skövde, Skövde, Sweden
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, UCL, London, UK
| | - Karen E Heath
- INGEMM, IdiPAZ and Skeletal Dysplasia Multidisciplinary Unit (UMDE, ERN-BOND), Hospital Universitario La Paz, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Homa Tajsharghi
- School of Health Sciences, Translational Medicine, University of Skövde, Skövde, Sweden
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Jenny C Taylor
- NIHR Biomedical Research Centre, Oxford, Oxfordshire, UK
- Wellcome Centre for Human Genetics, Oxford University, Oxford, Oxfordshire, UK
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25
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Villegas-Mirón P, Gallego A, Bertranpetit J, Laayouni H, Espinosa-Parrilla Y. Signatures of genetic variation in human microRNAs point to processes of positive selection and population-specific disease risks. Hum Genet 2022; 141:1673-1693. [PMID: 35249174 PMCID: PMC9522702 DOI: 10.1007/s00439-021-02423-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 05/30/2021] [Accepted: 12/19/2021] [Indexed: 12/11/2022]
Abstract
The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last 20 years. Most of them have been focused on the role of specific mutations in disease, while a minor proportion seek to analyse microRNA diversity in the genomes of human populations. We analyse the latest human microRNA annotations in the light of the most updated catalogue of genetic variation provided by the 1000 Genomes Project. By means of the in silico analysis of microRNA genetic variation we show that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or genomic location. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.
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Affiliation(s)
- Pablo Villegas-Mirón
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Alicia Gallego
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain.
| | - Yolanda Espinosa-Parrilla
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas, Chile.
- Laboratorio de Medicina Molecular-LMM, Centro Asistencial, Docente Y de Investigación-CADI, Universidad de Magallanes, Punta Arenas, Chile.
- Interuniversity Center on Healthy Aging, Punta Arenas, Chile.
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26
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Noblejas-López MDM, Gandullo-Sánchez L, Galán-Moya EM, López-Rosa R, Tébar-García D, Nieto-Jiménez C, Gómez-Juárez M, Burgos M, Pandiella A, Ocaña A. Antitumoral Activity of a CDK9 PROTAC Compound in HER2-Positive Breast Cancer. Int J Mol Sci 2022; 23:5476. [PMID: 35628286 PMCID: PMC9146359 DOI: 10.3390/ijms23105476] [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: 04/14/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are a broad family of proteins involved in the cell cycle and transcriptional regulation. In this article, we explore the antitumoral activity of a novel proteolysis-targeting chimera (PROTAC) compound against CDK9. Breast cancer cell lines from different subtypes were used. Transcriptomic mapping of CDKs in breast cancer demonstrated that the expression of CDK9 predicted a detrimental outcome in basal-like tumors (HR = 1.51, CI = 1.08-2.11, p = 0.015) and, particularly, in the luminal B subtype with HER2+ expression (HR = 1.82, CI = 1.17-2.82, p = 0.0069). The novel CDK9 PROTAC, THAL-SNS-032, displayed a profound inhibitory activity in MCF7, T47D, and BT474 cells, with less effect in SKBR3, HCC1569, HCC1954, MDA-MB-231, HS578T, and BT549 cells. The three cell lines with HER2 overexpression and no presence of ER, SKBR3, HCC1569, and HCC1954 displayed an EC50 three times higher compared to ER-positive and dual ER/HER2-positive cell lines. BT474-derived trastuzumab-resistant cell lines displayed a particular sensitivity to THAL-SNS-032. Western blot analyses showed that THAL-SNS-032 caused a decrease in CDK9 levels in BT474, BT474-RH, and BT474-TDM1R cells, and a significant increase in apoptosis. Experiments in animals demonstrated an inverse therapeutic index of THAL-SNS-032, with doses in the nontherapeutic and toxic range. The identified toxicity was mainly due to an on-target off-tumor effect of the compound in the gastrointestinal epithelium. In summary, the potent and efficient antitumoral properties of the CDK9 PROTAC THAL-SNS-032 opens the possibility of using this type of compound in breast cancer only if specifically delivered to cancer cells, particularly in ER/HER2-positive and HER2-resistant tumors.
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Affiliation(s)
- María del Mar Noblejas-López
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
- Centro Regional de Investigaciones Biomédicas (CRIB), Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
| | - Lucía Gandullo-Sánchez
- Instituto de Biología Molecular y Celular del Cáncer, CSIC, IBSAL and CIBERONC, 37007 Salamanca, Spain; (L.G.-S.); (A.P.)
| | - Eva M. Galán-Moya
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
- Centro Regional de Investigaciones Biomédicas (CRIB), Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
- Faculty of Nursing, Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
| | - Raquel López-Rosa
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
- Centro Regional de Investigaciones Biomédicas (CRIB), Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
| | - David Tébar-García
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
- Centro Regional de Investigaciones Biomédicas (CRIB), Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
| | - Cristina Nieto-Jiménez
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain;
| | - Mónica Gómez-Juárez
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
| | - Miguel Burgos
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
- Centro Regional de Investigaciones Biomédicas (CRIB), Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
- Department of Nutrition, Food Science and Physiology, School of Pharmacy and Nutrition, University of Navarra, 31008 Pamplona, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer, CSIC, IBSAL and CIBERONC, 37007 Salamanca, Spain; (L.G.-S.); (A.P.)
| | - Alberto Ocaña
- Translational Research Unit, Albacete University Hospital, 02008 Albacete, Spain; (M.d.M.N.-L.); (E.M.G.-M.); (R.L.-R.); (D.T.-G.); (M.G.-J.); (M.B.)
- Centro Regional de Investigaciones Biomédicas (CRIB), Castilla-La Mancha University (UCLM), 02008 Albacete, Spain
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC) and CIBERONC, 28040 Madrid, Spain;
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27
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Chambers JE, Zubkov N, Kubánková M, Nixon-Abell J, Mela I, Abreu S, Schwiening M, Lavarda G, López-Duarte I, Dickens JA, Torres T, Kaminski CF, Holt LJ, Avezov E, Huntington JA, George-Hyslop PS, Kuimova MK, Marciniak SJ. Z-α 1-antitrypsin polymers impose molecular filtration in the endoplasmic reticulum after undergoing phase transition to a solid state. Sci Adv 2022; 8:eabm2094. [PMID: 35394846 PMCID: PMC8993113 DOI: 10.1126/sciadv.abm2094] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/16/2022] [Indexed: 05/06/2023]
Abstract
Misfolding of secretory proteins in the endoplasmic reticulum (ER) features in many human diseases. In α1-antitrypsin deficiency, the pathogenic Z variant aberrantly assembles into polymers in the hepatocyte ER, leading to cirrhosis. We show that α1-antitrypsin polymers undergo a liquid:solid phase transition, forming a protein matrix that retards mobility of ER proteins by size-dependent molecular filtration. The Z-α1-antitrypsin phase transition is promoted during ER stress by an ATF6-mediated unfolded protein response. Furthermore, the ER chaperone calreticulin promotes Z-α1-antitrypsin solidification and increases protein matrix stiffness. Single-particle tracking reveals that solidification initiates in cells with normal ER morphology, previously assumed to represent a healthy pool. We show that Z-α1-antitrypsin-induced hypersensitivity to ER stress can be explained by immobilization of ER chaperones within the polymer matrix. This previously unidentified mechanism of ER dysfunction provides a template for understanding a diverse group of related proteinopathies and identifies ER chaperones as potential therapeutic targets.
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Affiliation(s)
- Joseph E. Chambers
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Nikita Zubkov
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Markéta Kubánková
- Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, UK
| | - Jonathon Nixon-Abell
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Susana Abreu
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Max Schwiening
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Giulia Lavarda
- Departamento de Química Orgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ismael López-Duarte
- Departamento de Química Orgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jennifer A. Dickens
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Tomás Torres
- Departamento de Química Orgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- IMDEA Nanociencia, Campus de Cantoblanco, Madrid 28049, Spain
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Grossman School of Medicine, 435 E 30th St, New York, NY 10016, USA
| | - Edward Avezov
- Department of Clinical Neurosciences and UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - James A. Huntington
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine (Neurology), Temerty Faculty of Medicine, University of Toronto, University Health Network, Toronto, ON M5T 0S8, Canada
- Taub Institute For Research on Alzheimer’s Disease and the Ageing Brain, Department of Neurology, Columbia University Irvine Medical Center, 630 West 1/68 Street, New York, NY 10032, USA
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, UK
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Royal Papworth Hospital, Cambridge CB2 0AY, UK
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28
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Wang P, Zhang J, Luan CY, Um M, Wang Y, Qiao M, Xie T, Zhang JN, Cabello A, Kim K. Significant loophole-free test of Kochen-Specker contextuality using two species of atomic ions. Sci Adv 2022; 8:eabk1660. [PMID: 35138888 PMCID: PMC8827658 DOI: 10.1126/sciadv.abk1660] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/16/2021] [Indexed: 05/28/2023]
Abstract
Quantum measurements cannot be thought of as revealing preexisting results, even when they do not disturb any other measurement in the same trial. This feature is called contextuality and is crucial for the quantum advantage in computing. Here, we report the observation of quantum contextuality simultaneously free of the detection, sharpness, and compatibility loopholes. The detection and sharpness loopholes are closed by adopting a hybrid two-ion system and highly efficient fluorescence measurements offering a detection efficiency of 100% and a measurement repeatability of >98%. The compatibility loophole is closed by targeting correlations between observables for two different ions in a Paul trap, a 171Yb+ ion and a 138Ba+ ion, chosen so measurements on each ion use different operation laser wavelengths, fluorescence wavelengths, and detectors. The experimental results show a violation of the bound for the most adversarial noncontextual models and open a way to certify quantum systems.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Low Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, People’s Republic of China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, People’s Republic of China
| | - Junhua Zhang
- Shenzhen Institute for Quantum Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People’s Republic of China
| | - Chun-Yang Luan
- State Key Laboratory of Low Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Mark Um
- State Key Laboratory of Low Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Ye Wang
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Mu Qiao
- State Key Laboratory of Low Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Tian Xie
- Kavli Nanoscience Institute and Thomas J. Watson Sr., Laboratory of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jing-Ning Zhang
- Beijing Academy of Quantum Information Sciences, Beijing 100193, People’s Republic of China
| | - Adán Cabello
- Departamento de Física Aplicada II, Universidad de Sevilla, E-41012 Sevilla, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Kihwan Kim
- State Key Laboratory of Low Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, People’s Republic of China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, People’s Republic of China
- Frontier Science Center for Quantum Information, Beijing 100084, People’s Republic of China
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29
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Brañas-Garza P, Jorrat D, Alfonso A, Espín AM, Muñoz TG, Kovářík J. Exposure to the COVID-19 pandemic environment and generosity. R Soc Open Sci 2022; 9:210919. [PMID: 35070340 PMCID: PMC8753156 DOI: 10.1098/rsos.210919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/09/2021] [Indexed: 05/30/2023]
Abstract
We report data from an online experiment which allows us to study how generosity changed over a 6-day period during the initial explosive growth of the COVID-19 pandemic in Andalusia, Spain, while the country was under a strict lockdown. Participants (n = 969) could donate a fraction of a €100 prize to an unknown charity. Our data are particularly rich in the age distribution and we complement them with daily public information about COVID-19-related deaths, infections and hospital admissions. We find correlational evidence that donations decreased in the period under study, particularly among older individuals. Our analysis of the mechanisms behind the detected decrease in generosity suggests that expectations about others' behaviour, perceived mortality risk and (alarming) information play a key-but independent-role for behavioural adaptation. These results indicate that social behaviour is quickly adjusted in response to the pandemic environment, possibly reflecting some form of selective prosociality.
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Affiliation(s)
- P. Brañas-Garza
- Loyola Behavioral Lab & Department of Economics, Universidad Loyola Andalucía, Sevilla, Spain
| | - D. Jorrat
- Loyola Behavioral Lab & Department of Economics, Universidad Loyola Andalucía, Sevilla, Spain
| | - A. Alfonso
- Loyola Behavioral Lab & Department of Economics, Universidad Loyola Andalucía, Sevilla, Spain
| | - A. M. Espín
- Department of Anthropology, Universidad de Granada, Spain
| | - T. García Muñoz
- Department of Quantitative Economics, Universidad de Granada, Spain
| | - J. Kovářík
- Universidad del País Vasco UPV-EHU, Bilbao, Spain
- CERGE-EI, Prague, Czech Republic
- Faculty of Economics and Faculty of Arts, University of West Bohemia, Pilsen, Czech Republic
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Cortell-Nicolau A, García-Puchol O, Barrera-Cruz M, García-Rivero D. The spread of agriculture in Iberia through Approximate Bayesian Computation and Neolithic projectile tools. PLoS One 2021; 16:e0261813. [PMID: 34962962 PMCID: PMC8714124 DOI: 10.1371/journal.pone.0261813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/21/2021] [Accepted: 12/13/2021] [Indexed: 11/18/2022] Open
Abstract
In the present article we use geometric microliths (a specific type of arrowhead) and Approximate Bayesian Computation (ABC) in order to evaluate possible origin points and expansion routes for the Neolithic in the Iberian Peninsula. In order to do so, we divide the Iberian Peninsula in four areas (Ebro river, Catalan shores, Xúquer river and Guadalquivir river) and we sample the geometric microliths existing in the sites with the oldest radiocarbon dates for each zone. On this data, we perform a partial Mantel test with three matrices: geographic distance matrix, cultural distance matrix and chronological distance matrix. After this is done, we simulate a series of partial Mantel tests where we alter the chronological matrix by using an expansion model with randomised origin points, and using the distribution of the observed partial Mantel test’s results as a summary statistic within an Approximate Bayesian Computation-Sequential Monte-Carlo (ABC-SMC) algorithm framework. Our results point clearly to a Neolithic expansion route following the Northern Mediterranean, whilst the Southern Mediterranean route could also find support and should be further discussed. The most probable origin points focus on the Xúquer river area.
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Affiliation(s)
- Alfredo Cortell-Nicolau
- Departament de Prehistòria, Arqueologia i Història Antiga, Facultat de Geografia i Història, Universitat de València, València, Spain
- Department of Archaeology, McDonald Institute for Archaeological Research, Faculty of Human, Social, and Political Science, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (OGP); (ACN)
| | - Oreto García-Puchol
- Departament de Prehistòria, Arqueologia i Història Antiga, Facultat de Geografia i Història, Universitat de València, València, Spain
- * E-mail: (OGP); (ACN)
| | - María Barrera-Cruz
- Departament de Prehistòria, Arqueologia i Història Antiga, Facultat de Geografia i Història, Universitat de València, València, Spain
| | - Daniel García-Rivero
- Department of Prehistory and Archaeology, Faculty of Geography and History, University of Seville, Seville, Spain
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Chini A, Monte I, Fernández-Barbero G, Boter M, Hicks G, Raikhel N, Solano R. A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and nonvascular plants. Plant Physiol 2021; 187:1399-1413. [PMID: 34618088 PMCID: PMC8566257 DOI: 10.1093/plphys/kiab369] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/03/2021] [Indexed: 05/12/2023]
Abstract
The phytohormone jasmonoyl-L-isoleucine (JA-Ile) regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein Coronatine Insensitive 1 (COI1) and a Jasmonate (JA) ZIM-domain (JAZ) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signaling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI-JAZ interaction and degradation of JAZ1 and JAZ9 in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation, and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana) COI1-JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1-JAZ also occurs in the liverwort Marchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signaling, J4 works as an antagonist of the closely related auxin signaling pathway, preventing Transport Inhibitor Response1/Aux-indole-3-acetic acid interaction and auxin responses in planta, including hormone-mediated degradation of an auxin repressor, gene expression, and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways. One-sentence summary: A chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and nonvascular plants.
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Affiliation(s)
- Andrea Chini
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
- Author for correspondence:
| | - Isabel Monte
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
- Present address: Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, 8008, Switzerland
| | - Gemma Fernández-Barbero
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
| | - Marta Boter
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
- Present address: Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Glenn Hicks
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, 92521, USA
| | - Natasha Raikhel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, 92521, USA
| | - Roberto Solano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
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Cueto-Díaz EJ, Castro-Muñiz A, Suárez-García F, Gálvez-Martínez S, Torquemada-Vico MC, Valles-González MP, Mateo-Martí E. APTES-Based Silica Nanoparticles as a Potential Modifier for the Selective Sequestration of CO 2 Gas Molecules. Nanomaterials (Basel) 2021; 11:2893. [PMID: 34835658 PMCID: PMC8620991 DOI: 10.3390/nano11112893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/31/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
In this work, we have described the characterization of hybrid silica nanoparticles of 50 nm size, showing outstanding size homogeneity, a large surface area, and remarkable CO2 sorption/desorption capabilities. A wide battery of techniques was conducted ranging from spectroscopies such as: UV-Vis and IR, to microscopies (SEM, AFM) and CO2 sorption/desorption isotherms, thus with the purpose of the full characterization of the material. The bare SiO2 (50 nm) nanoparticles modified with 3-aminopropyl (triethoxysilane), APTES@SiO2 (50 nm), show a remarkable CO2 sequestration enhancement compared to the pristine material (0.57 vs. 0.80 mmol/g respectively at 50 °C). Furthermore, when comparing them to their 200 nm size counterparts (SiO2 (200 nm) and APTES@SiO2 (200 nm)), there is a marked CO2 capture increment as a consequence of their significantly larger micropore volume (0.25 cm3/g). Additionally, ideal absorbed solution theory (IAST) was conducted to determine the CO2/N2 selectivity at 25 and 50 °C of the four materials of study, which turned out to be >70, being in the range of performance of the most efficient microporous materials reported to date, even surpassing those based on silica.
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Affiliation(s)
- Eduardo J. Cueto-Díaz
- Centro de Astrobiología, (INTA-CSIC), Ctra. Ajalvir, Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain; (S.G.-M.); (E.M.-M.)
| | - Alberto Castro-Muñiz
- Instituto de Ciencia y Tecnología del Carbono (INCAR-CSIC), C/ Francisco Pintado Fe, 26, 33011 Oviedo, Spain; (A.C.-M.); (F.S.-G.)
| | - Fabián Suárez-García
- Instituto de Ciencia y Tecnología del Carbono (INCAR-CSIC), C/ Francisco Pintado Fe, 26, 33011 Oviedo, Spain; (A.C.-M.); (F.S.-G.)
| | - Santos Gálvez-Martínez
- Centro de Astrobiología, (INTA-CSIC), Ctra. Ajalvir, Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain; (S.G.-M.); (E.M.-M.)
| | - Mª Carmen Torquemada-Vico
- Departamento de Óptica Espacial, Instituto Nacional de Técnica Aeroespacial, Ctra. Ajalvir, Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain;
| | - Mª Pilar Valles-González
- Departamento de Materiales y Estructuras, Instituto Nacional de Técnica Aeroespacial, Ctra. Ajalvir, Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain;
| | - Eva Mateo-Martí
- Centro de Astrobiología, (INTA-CSIC), Ctra. Ajalvir, Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain; (S.G.-M.); (E.M.-M.)
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Domínguez-Andrés J, Kuijpers Y, Bakker OB, Jaeger M, Xu CJ, Van der Meer JWM, Jakobsson M, Bertranpetit J, Joosten LAB, Li Y, Netea MG. Evolution of cytokine production capacity in ancient and modern European populations. eLife 2021; 10:e64971. [PMID: 34488939 PMCID: PMC8423439 DOI: 10.7554/elife.64971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/30/2021] [Indexed: 12/17/2022] Open
Abstract
As our ancestors migrated throughout different continents, natural selection increased the presence of alleles advantageous in the new environments. Heritable variations that alter the susceptibility to diseases vary with the historical period, the virulence of the infections, and their geographical spread. In this study we built polygenic scores for heritable traits that influence the genetic adaptation in the production of cytokines and immune-mediated disorders, including infectious, inflammatory, and autoimmune diseases, and applied them to the genomes of several ancient European populations. We observed that the advent of the Neolithic was a turning point for immune-mediated traits in Europeans, favoring those alleles linked with the development of tolerance against intracellular pathogens and promoting inflammatory responses against extracellular microbes. These evolutionary patterns are also associated with an increased presence of traits related to inflammatory and auto-immune diseases.
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Affiliation(s)
- Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), RadboudUniversity Medical CenterNijmegenNetherlands
| | - Yunus Kuijpers
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH)HannoverGermany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH)HannoverGermany
| | - Olivier B Bakker
- Department of Genetics, University Medical Centre GroningenNijmegenNetherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), RadboudUniversity Medical CenterNijmegenNetherlands
| | - Cheng-Jian Xu
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH)HannoverGermany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH)HannoverGermany
| | - Jos WM Van der Meer
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala UniversityUppsalaSweden
- Centre for Anthropological Research, Department of Anthropology and Development Studies, University of JohannesburgAuckland ParkSouth Africa
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu FabraBarcelonaSpain
| | - Leo AB Joosten
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), RadboudUniversity Medical CenterNijmegenNetherlands
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), RadboudUniversity Medical CenterNijmegenNetherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH)HannoverGermany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH)HannoverGermany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical CentreNijmegenNetherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), RadboudUniversity Medical CenterNijmegenNetherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of BonnBonnGermany
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Abstract
Photodynamic therapy (PDT) is becoming a promising way to treat various kinds of cancers, with few side effects. Porphyrinoids are the most relevant photosensitizers (PS) in PDT, because they present high extinction coefficients, biocompatibility, and excellent photochemical behavior. To maximize therapeutic effects, polymer-PS conjugates, and PS-loaded nanoparticles have been developed, with insights in improving tumor delivery. However, some drawbacks such as non-biodegradability, multistep fabrication, and low reagent loadings limit their clinical application. A novel strategy, noted by some authors as the "one-for-all" approach, is emerging to circumvent the use of additional delivery agents. This approach relies on the self-assembly of amphiphilic PS to fabricate nanostructures with improved transport properties. In this review we focus on different rational designs of porphyrinoid PS to achieve some of the following attributes in nanoassembly: i) selective uptake, through the incorporation of recognizable biological vectors; ii) responsiveness to stimuli; iii) combination of imaging and therapeutic functions; and iv) multimodal therapy, including photothermal or chemotherapy abilities.
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Affiliation(s)
- Irene Paramio
- Department of Organic ChemistryUniversidad Autónoma de MadridC/Francisco Tomás y Valiente 728049MadridSpain
| | - Tomás Torres
- Department of Organic ChemistryUniversidad Autónoma de MadridC/Francisco Tomás y Valiente 728049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridC/Francisco Tomás y Valiente 728049MadridSpain
- Instituto Madrileño de Estudios Avanzados (IMDEA)-NanocienciaC/Faraday 928049MadridSpain
| | - Gema de la Torre
- Department of Organic ChemistryUniversidad Autónoma de MadridC/Francisco Tomás y Valiente 728049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridC/Francisco Tomás y Valiente 728049MadridSpain
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Morelli L, Paulišić S, Qin W, Iglesias-Sanchez A, Roig-Villanova I, Florez-Sarasa I, Rodriguez-Concepcion M, Martinez-Garcia JF. Light signals generated by vegetation shade facilitate acclimation to low light in shade-avoider plants. Plant Physiol 2021; 186:2137-2151. [PMID: 34618102 PMCID: PMC8331150 DOI: 10.1093/plphys/kiab206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/08/2021] [Indexed: 05/27/2023]
Abstract
When growing in search for light, plants can experience continuous or occasional shading by other plants. Plant proximity causes a decrease in the ratio of R to far-red light (low R:FR) due to the preferential absorbance of R light and reflection of FR light by photosynthetic tissues of neighboring plants. This signal is often perceived before actual shading causes a reduction in photosynthetically active radiation (low PAR). Here, we investigated how several Brassicaceae species from different habitats respond to low R:FR and low PAR in terms of elongation, photosynthesis, and photoacclimation. Shade-tolerant plants such as hairy bittercress (Cardamine hirsuta) displayed a good adaptation to low PAR but a poor or null response to low R:FR exposure. In contrast, shade-avoider species, such as Arabidopsis (Arabidopsis thaliana), showed a weak photosynthetic performance under low PAR but they strongly elongated when exposed to low R:FR. These responses could be genetically uncoupled. Most interestingly, exposure to low R:FR of shade-avoider (but not shade-tolerant) plants improved their photoacclimation to low PAR by triggering changes in photosynthesis-related gene expression, pigment accumulation, and chloroplast ultrastructure. These results indicate that low R:FR signaling unleashes molecular, metabolic, and developmental responses that allow shade-avoider plants (including most crops) to adjust their photosynthetic capacity in anticipation of eventual shading by nearby plants.
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Affiliation(s)
- Luca Morelli
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Wenting Qin
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Ariadna Iglesias-Sanchez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Irma Roig-Villanova
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Manuel Rodriguez-Concepcion
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Jaime F Martinez-Garcia
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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Morales-Amador A, Molina-Miras A, López-Rosales L, Sánchez-Mirón A, García-Camacho F, Souto ML, Fernández JJ. Isolation and Structural Elucidation of New Amphidinol Analogues from Amphidinium carterae Cultivated in a Pilot-Scale Photobioreactor. Mar Drugs 2021; 19:432. [PMID: 34436271 PMCID: PMC8399002 DOI: 10.3390/md19080432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/07/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
The demand for valuable products from dinoflagellate biotechnology has increased remarkably in recent years due to their many prospective applications. However, there remain many challenges that need to be addressed in order to make dinoflagellate bioactives a commercial reality. In this article, we describe the technical feasibility of producing and recovering amphidinol analogues (AMs) excreted into a culture broth of Amphidinium carterae ACRN03, successfully cultured in an LED-illuminated pilot-scale (80 L) bubble column photobioreactor operated in fed-batch mode with a pulse feeding strategy. We report on the isolation of new structurally related AMs, amphidinol 24 (1, AM24), amphidinol 25 (2, AM25) and amphidinol 26 (3, AM26), from a singular fraction resulting from the downstream processing. Their planar structures were elucidated by extensive NMR and HRMS analysis, whereas the relative configuration of the C-32→C-47 bis-tetrahydropyran core was confirmed to be antipodal in accord with the recently revised configuration of AM3. The hemolytic activities of the new metabolites and other related derivatives were evaluated, and structure-activity conclusions were established. Their isolation was based on a straightforward and high-performance bioprocess that could be suitable for the commercial development of AMs or other high-value compounds from shear sensitive dinoflagellates.
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Affiliation(s)
- Adrián Morales-Amador
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Spain;
- Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Spain
| | - Alejandro Molina-Miras
- Chemical Engineering Department, University of Almería, 04120 Almería, Spain; (A.M.-M.); (L.L.-R.); (A.S.-M.); (F.G.-C.)
- Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Lorenzo López-Rosales
- Chemical Engineering Department, University of Almería, 04120 Almería, Spain; (A.M.-M.); (L.L.-R.); (A.S.-M.); (F.G.-C.)
- Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Asterio Sánchez-Mirón
- Chemical Engineering Department, University of Almería, 04120 Almería, Spain; (A.M.-M.); (L.L.-R.); (A.S.-M.); (F.G.-C.)
- Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - Francisco García-Camacho
- Chemical Engineering Department, University of Almería, 04120 Almería, Spain; (A.M.-M.); (L.L.-R.); (A.S.-M.); (F.G.-C.)
- Research Center CIAIMBITAL, University of Almería, 04120 Almería, Spain
| | - María L. Souto
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Spain;
- Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Spain
| | - José J. Fernández
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Spain;
- Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Spain
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Calvo P, Martínez-Jiménez MI, Díaz M, Stojkovic G, Kasho K, Guerra S, Wanrooij S, Méndez J, Blanco L. Motif WFYY of human PrimPol is crucial to stabilize the incoming 3'-nucleotide during replication fork restart. Nucleic Acids Res 2021; 49:8199-8213. [PMID: 34302490 PMCID: PMC8373064 DOI: 10.1093/nar/gkab634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/12/2022] Open
Abstract
PrimPol is the second primase in human cells, the first with the ability to start DNA chains with dNTPs. PrimPol contributes to DNA damage tolerance by restarting DNA synthesis beyond stalling lesions, acting as a TLS primase. Multiple alignment of eukaryotic PrimPols allowed us to identify a highly conserved motif, WxxY near the invariant motif A, which contains two active site metal ligands in all members of the archeo-eukaryotic primase (AEP) superfamily. In vivo and in vitro analysis of single variants of the WFYY motif of human PrimPol demonstrated that the invariant Trp87 and Tyr90 residues are essential for both primase and polymerase activities, mainly due to their crucial role in binding incoming nucleotides. Accordingly, the human variant F88L, altering the WFYY motif, displayed reduced binding of incoming nucleotides, affecting its primase/polymerase activities especially during TLS reactions on UV-damaged DNA. Conversely, the Y89D mutation initially associated with High Myopia did not affect the ability to rescue stalled replication forks in human cells. Collectively, our data suggest that the WFYY motif has a fundamental role in stabilizing the incoming 3′-nucleotide, an essential requisite for both its primase and TLS abilities during replication fork restart.
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Affiliation(s)
- Patricia A Calvo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049, Madrid, Spain
| | | | - Marcos Díaz
- Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Gorazd Stojkovic
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Susana Guerra
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049, Madrid, Spain
| | - Sjoerd Wanrooij
- Correspondence may also be addressed to Sjoerd Wanrooij. Tel: +46 722460309;
| | - Juan Méndez
- Correspondence may also be addressed to Juan Méndez. Tel: +34 917328000; Fax: +34 917328033;
| | - Luis Blanco
- To whom correspondence should be addressed. Tel: +34 911964685; Fax: +34 911964401;
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Escamilla P, Viciano-Chumillas M, Bruno R, Armentano D, Pardo E, Ferrando-Soria J. Photodegradation of Brilliant Green Dye by a Zinc bioMOF and Crystallographic Visualization of Resulting CO 2. Molecules 2021; 26:4098. [PMID: 34279437 PMCID: PMC8272194 DOI: 10.3390/molecules26134098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
We present a novel bio-friendly water-stable Zn-based MOF (1), derived from the natural amino acid L-serine, which was able to efficiently photodegrade water solutions of brilliant green dye in only 120 min. The total degradation was followed by UV-Vis spectroscopy and further confirmed by single-crystal X-ray crystallography, revealing the presence of CO2 within its channels. Reusability studies further demonstrate the structural and performance robustness of 1.
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Affiliation(s)
- Paula Escamilla
- Departament de Química Inorgànica, Instituto de Ciencia Molecular (ICMOL), Universitat de València, Paterna, 46980 València, Spain; (P.E.); (M.V.-C.)
| | - Marta Viciano-Chumillas
- Departament de Química Inorgànica, Instituto de Ciencia Molecular (ICMOL), Universitat de València, Paterna, 46980 València, Spain; (P.E.); (M.V.-C.)
| | - Rosaria Bruno
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Cosenza, Italy;
| | - Donatella Armentano
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Cosenza, Italy;
| | - Emilio Pardo
- Departament de Química Inorgànica, Instituto de Ciencia Molecular (ICMOL), Universitat de València, Paterna, 46980 València, Spain; (P.E.); (M.V.-C.)
| | - Jesús Ferrando-Soria
- Departament de Química Inorgànica, Instituto de Ciencia Molecular (ICMOL), Universitat de València, Paterna, 46980 València, Spain; (P.E.); (M.V.-C.)
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Almeida‐Marrero V, Mascaraque M, Jesús Vicente‐Arana M, Juarranz Á, Torres T, de la Escosura A. Tuning the Nanoaggregates of Sialylated Biohybrid Photosensitizers for Intracellular Activation of the Photodynamic Response. Chemistry 2021; 27:9634-9642. [PMID: 33834569 PMCID: PMC8360122 DOI: 10.1002/chem.202100681] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/24/2021] [Indexed: 01/18/2023]
Abstract
In the endeavor of extending the clinical use of photodynamic therapy (PDT) for the treatment of superficial cancers and other neoplastic diseases, deeper knowledge and control of the subcellular processes that determine the response of photosensitizers (PS) are needed. Recent strategies in this direction involve the use of activatable and nanostructured PS. Here, both capacities have been tuned in two dendritic zinc(II) phthalocyanine (ZnPc) derivatives, either asymmetrically or symmetrically substituted with 3 and 12 copies of the carbohydrate sialic acid (SA), respectively. Interestingly, the amphiphilic ZnPc-SA biohybrid (1) self-assembles into well-defined nanoaggregates in aqueous solution, facilitating cellular internalization and transport whereas the PS remains inactive. Within the cells, these nanostructured hybrids localize in the lysosomes, as usually happens for anionic and hydrophilic aggregated PS. Yet, in contrast to most of them (e. g., compound 2), hybrid 1 recovers the capacity for photoinduced ROS generation within the target organelles due to its amphiphilic character; this allows disruption of aggregation when the compound is inserted into the lysosomal membrane, with the concomitant highly efficient PDT response.
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Affiliation(s)
- Verónica Almeida‐Marrero
- Department of Organic Chemistry / SIdI (MJVA)Universidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
| | - Marta Mascaraque
- Departamento de BiologíaUniversidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS)28034MadridSpain
| | - María Jesús Vicente‐Arana
- Department of Organic Chemistry / SIdI (MJVA)Universidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
| | - Ángeles Juarranz
- Departamento de BiologíaUniversidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS)28034MadridSpain
| | - Tomás Torres
- Department of Organic Chemistry / SIdI (MJVA)Universidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Campus de Cantoblanco28049MadridSpain
- IMDEA NanoscienceCampus de Cantoblanco28049MadridSpain
| | - Andrés de la Escosura
- Department of Organic Chemistry / SIdI (MJVA)Universidad Autónoma de MadridCampus de Cantoblanco28049MadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Campus de Cantoblanco28049MadridSpain
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Wright RJ, Bosch R, Langille MGI, Gibson MI, Christie-Oleza JA. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere. Microbiome 2021; 9:141. [PMID: 34154652 PMCID: PMC8215760 DOI: 10.1186/s40168-021-01054-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 10/28/2020] [Accepted: 03/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. RESULTS We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. CONCLUSIONS Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Rafael Bosch
- University of the Balearic Islands, Palma, Spain
- IMEDEA (CSIC-UIB), Esporles, Spain
| | - Morgan G. I. Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, UK
- University of the Balearic Islands, Palma, Spain
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Vázquez‐González V, Mayoral MJ, Aparicio F, Martínez‐Arjona P, González‐Rodríguez D. The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers. Chempluschem 2021; 86:1087-1096. [PMID: 34185949 PMCID: PMC8457134 DOI: 10.1002/cplu.202100255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/11/2021] [Indexed: 11/29/2022]
Abstract
Nanotubes are a fascinating kind of self-assembled structure which have a wide interest and potential in supramolecular chemistry. We demonstrated that nanotubes of defined dimensions can be produced from dinucleobase monomers through two decoupled hierarchical cooperative processes: cyclotetramerization and supramolecular polymerization. Here we analyze the role of peripheral amide groups, which can form an array of hydrogen bonds along the tube axis, on this self-assembly process. A combination of 1 H NMR and CD spectroscopy techniques allowed us to analyze quantitatively the thermodynamics of each of these two processes separately. We found out that the presence of these amide directors is essential to guide the polymerization event and that their nature and number have a strong influence, not only on the stabilization of the stacks of macrocycles, but also on the supramolecular polymerization mechanism.
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Affiliation(s)
- Violeta Vázquez‐González
- Nanostructured Molecular Systems and Materials GroupOrganic Chemistry DepartmentScience FacultyUniversidad Autónoma de Madrid28049MadridSpain
| | - María J. Mayoral
- Nanostructured Molecular Systems and Materials GroupOrganic Chemistry DepartmentScience FacultyUniversidad Autónoma de Madrid28049MadridSpain
- Inorganic Chemistry DepartmentChemistry FacultyUniversidad Complutense de Madrid28040MadridSpain
| | - Fátima Aparicio
- Nanostructured Molecular Systems and Materials GroupOrganic Chemistry DepartmentScience FacultyUniversidad Autónoma de Madrid28049MadridSpain
| | - Paula Martínez‐Arjona
- Nanostructured Molecular Systems and Materials GroupOrganic Chemistry DepartmentScience FacultyUniversidad Autónoma de Madrid28049MadridSpain
| | - David González‐Rodríguez
- Nanostructured Molecular Systems and Materials GroupOrganic Chemistry DepartmentScience FacultyUniversidad Autónoma de Madrid28049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de Madrid28049MadridSpain
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Villanueva-Paz M, Morán L, López-Alcántara N, Freixo C, Andrade RJ, Lucena MI, Cubero FJ. Oxidative Stress in Drug-Induced Liver Injury (DILI): From Mechanisms to Biomarkers for Use in Clinical Practice. Antioxidants (Basel) 2021; 10:390. [PMID: 33807700 PMCID: PMC8000729 DOI: 10.3390/antiox10030390] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Idiosyncratic drug-induced liver injury (DILI) is a type of hepatic injury caused by an uncommon drug adverse reaction that can develop to conditions spanning from asymptomatic liver laboratory abnormalities to acute liver failure (ALF) and death. The cellular and molecular mechanisms involved in DILI are poorly understood. Hepatocyte damage can be caused by the metabolic activation of chemically active intermediate metabolites that covalently bind to macromolecules (e.g., proteins, DNA), forming protein adducts-neoantigens-that lead to the generation of oxidative stress, mitochondrial dysfunction, and endoplasmic reticulum (ER) stress, which can eventually lead to cell death. In parallel, damage-associated molecular patterns (DAMPs) stimulate the immune response, whereby inflammasomes play a pivotal role, and neoantigen presentation on specific human leukocyte antigen (HLA) molecules trigger the adaptive immune response. A wide array of antioxidant mechanisms exists to counterbalance the effect of oxidants, including glutathione (GSH), superoxide dismutase (SOD), catalase, and glutathione peroxidase (GPX), which are pivotal in detoxification. These get compromised during DILI, triggering an imbalance between oxidants and antioxidants defense systems, generating oxidative stress. As a result of exacerbated oxidative stress, several danger signals, including mitochondrial damage, cell death, and inflammatory markers, and microRNAs (miRNAs) related to extracellular vesicles (EVs) have already been reported as mechanistic biomarkers. Here, the status quo and the future directions in DILI are thoroughly discussed, with a special focus on the role of oxidative stress and the development of new biomarkers.
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Affiliation(s)
- Marina Villanueva-Paz
- Unidad de Gestión Clínica de Gastroenterología, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, 29071 Málaga, Spain; (M.V.-P.); (M.I.L.)
| | - Laura Morán
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, 28040 Madrid, Spain; (L.M.); (N.L.-A.)
- Health Research Institute Gregorio Marañón (IiSGM), 28009 Madrid, Spain
| | - Nuria López-Alcántara
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, 28040 Madrid, Spain; (L.M.); (N.L.-A.)
| | - Cristiana Freixo
- CINTESIS, Center for Health Technology and Services Research, do Porto University School of Medicine, 4200-319 Porto, Portugal;
| | - Raúl J. Andrade
- Unidad de Gestión Clínica de Gastroenterología, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, 29071 Málaga, Spain; (M.V.-P.); (M.I.L.)
| | - M Isabel Lucena
- Unidad de Gestión Clínica de Gastroenterología, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, 29071 Málaga, Spain; (M.V.-P.); (M.I.L.)
| | - Francisco Javier Cubero
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, 28040 Madrid, Spain; (L.M.); (N.L.-A.)
- 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain
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Rebollo B, Telenczuk B, Navarro-Guzman A, Destexhe A, Sanchez-Vives MV. Modulation of intercolumnar synchronization by endogenous electric fields in cerebral cortex. Sci Adv 2021; 7:7/10/eabc7772. [PMID: 33658192 PMCID: PMC7929504 DOI: 10.1126/sciadv.abc7772] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/21/2021] [Indexed: 06/01/2023]
Abstract
Neurons synaptically interacting in a conductive medium generate extracellular endogenous electric fields (EFs) that reciprocally affect membrane potential. Exogenous EFs modulate neuronal activity, and their clinical applications are being profusely explored. However, whether endogenous EFs contribute to network synchronization remains unclear. We analyzed spontaneously generated slow-wave activity in the cerebral cortex network in vitro, which allowed us to distinguish synaptic from nonsynaptic mechanisms of activity propagation and synchronization. Slow oscillations generated EFs that propagated independently of synaptic transmission. We demonstrate that cortical oscillations modulate spontaneous rhythmic activity of neighboring synaptically disconnected cortical columns if layers are aligned. We provide experimental evidence that these EF-mediated effects are compatible with electric dipoles. With a model of interacting dipoles, we reproduce the experimental measurements and predict that endogenous EF-mediated synchronizing effects should be relevant in the brain. Thus, experiments and models suggest that electric-dipole interactions contribute to synchronization of neighboring cortical columns.
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Affiliation(s)
- Beatriz Rebollo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Bartosz Telenczuk
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences, Gif sur Yvette, France
| | - Alvaro Navarro-Guzman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alain Destexhe
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences, Gif sur Yvette, France
| | - Maria V Sanchez-Vives
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- ICREA, Barcelona, Spain
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Alegre-Cortés J, Sáez M, Montanari R, Reig R. Medium spiny neurons activity reveals the discrete segregation of mouse dorsal striatum. eLife 2021; 10:e60580. [PMID: 33599609 PMCID: PMC7924950 DOI: 10.7554/elife.60580] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 09/27/2020] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
Behavioral studies differentiate the rodent dorsal striatum (DS) into lateral and medial regions; however, anatomical evidence suggests that it is a unified structure. To understand striatal dynamics and basal ganglia functions, it is essential to clarify the circuitry that supports this behavioral-based segregation. Here, we show that the mouse DS is made of two non-overlapping functional circuits divided by a boundary. Combining in vivo optopatch-clamp and extracellular recordings of spontaneous and evoked sensory activity, we demonstrate different coupling of lateral and medial striatum to the cortex together with an independent integration of the spontaneous activity, due to particular corticostriatal connectivity and local attributes of each region. Additionally, we show differences in slow and fast oscillations and in the electrophysiological properties between striatonigral and striatopallidal neurons. In summary, these results demonstrate that the rodent DS is segregated in two neuronal circuits, in homology with the caudate and putamen nuclei of primates.
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Affiliation(s)
| | - María Sáez
- Instituto de Neurociencias CSIC-UMHSan Juan de AlicanteSpain
| | | | - Ramon Reig
- Instituto de Neurociencias CSIC-UMHSan Juan de AlicanteSpain
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Guzmán D, Papadopoulos I, Lavarda G, Rami PR, Tykwinski RR, Rodríguez‐Morgade MS, Guldi DM, Torres T. Controlling Intramolecular Förster Resonance Energy Transfer and Singlet Fission in a Subporphyrazine-Pentacene Conjugate by Solvent Polarity. Angew Chem Int Ed Engl 2021; 60:1474-1481. [PMID: 33002284 PMCID: PMC7839765 DOI: 10.1002/anie.202011197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Indexed: 11/24/2022]
Abstract
Due its complementary absorptions in the range of 450 and 600 nm, an energy-donating hexaaryl-subporphyrazine has been linked to a pentacene dimer, which acts primarily as an energy acceptor and secondarily as a singlet fission enabler. In the corresponding conjugate, efficient intramolecular Förster resonance energy transfer (i-FRET) is the modus operandi to transfer energy from the subporphyrazine to the pentacene dimer. Upon energy transfer, the pentacene dimer undergoes intramolecular singlet fission (i-SF), that is, converting the singlet excited state, via an intermediate state, into a pair of correlated triplet excited states. Solvatochromic fluorescence of the subporphyrazine is a key feature of this system and features a red-shift as large as 20 nm in polar media. Solvent is thus used to modulate spectral overlap between the fluorescence of subporphyrazine and absorption of the pentacene dimer, which controls the Förster rate constant, on one hand, and the triplet quantum yield, on the other hand. The optimum spectral overlap is realized in xylene, leading to Förster rate constant of 3.52×1011 s-1 and a triplet quantum yield of 171 % ±10 %. In short, the solvent polarity dependence, which is a unique feature of subporphyrazines, is decisive in terms of adjusting spectral overlap, ensuring a sizable Förster rate constant, and maximizing triplet quantum yields. Uniquely, this optimization can be achieved without a need for synthetic modification of the subporphyrazine donor.
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Affiliation(s)
- David Guzmán
- Departamento de Química OrgánicaUniversidad Autónoma de MadridCantoblanco28049MadridSpain
| | - Ilias Papadopoulos
- Department of Chemistry and PharmacyInterdisciplinary Center for Molecular Materials (ICMM)Friedrich-Alexander-Universität Erlangen-NürnbergEgerlandstr. 391058ErlangenGermany
| | - Giulia Lavarda
- Departamento de Química OrgánicaUniversidad Autónoma de MadridCantoblanco28049MadridSpain
| | - Parisa R. Rami
- Department of ChemistryUniversity of AlbertaEdmontonAlbertaT6G 2G2Canada
| | - Rik R. Tykwinski
- Department of ChemistryUniversity of AlbertaEdmontonAlbertaT6G 2G2Canada
| | - M. Salomé Rodríguez‐Morgade
- Departamento de Química OrgánicaUniversidad Autónoma de MadridCantoblanco28049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridCantoblanco28049MadridSpain
| | - Dirk M. Guldi
- Department of Chemistry and PharmacyInterdisciplinary Center for Molecular Materials (ICMM)Friedrich-Alexander-Universität Erlangen-NürnbergEgerlandstr. 391058ErlangenGermany
| | - Tomás Torres
- Departamento de Química OrgánicaUniversidad Autónoma de MadridCantoblanco28049MadridSpain
- IMDEA-NanocienciaCampus de Cantoblanco28049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridCantoblanco28049MadridSpain
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Huggett N, Lizzi F, Menon T. Missing the point in noncommutative geometry. Synthese 2021; 199:4695-4728. [PMID: 34866670 PMCID: PMC8604559 DOI: 10.1007/s11229-020-02998-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/10/2020] [Indexed: 06/13/2023]
Abstract
Noncommutative geometries generalize standard smooth geometries, parametrizing the noncommutativity of dimensions with a fundamental quantity with the dimensions of area. The question arises then of whether the concept of a region smaller than the scale-and ultimately the concept of a point-makes sense in such a theory. We argue that it does not, in two interrelated ways. In the context of Connes' spectral triple approach, we show that arbitrarily small regions are not definable in the formal sense. While in the scalar field Moyal-Weyl approach, we show that they cannot be given an operational definition. We conclude that points do not exist in such geometries. We therefore investigate (a) the metaphysics of such a geometry, and (b) how the appearance of smooth manifold might be recovered as an approximation to a fundamental noncommutative geometry.
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Affiliation(s)
- Nick Huggett
- Department of Philosophy, University of Illinois at Chicago, Chicago, IL USA
| | - Fedele Lizzi
- Dipartimento di Fisica “Ettore Pancini”, Università di Napoli Federico II, Napoli, Italy
- INFN, Sezione di Napoli, Napoli, Italy
- Departament de Física Quàntica i Astrofìsica and Institut de Cìences del Cosmos (ICCUB), Universitat de Barcelona, Barcelona, Spain
| | - Tushar Menon
- Faculty of Philosophy, University of Cambridge, Cambridge, UK
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Ramallo-González AP, González-Vidal A, Skarmeta AF. CIoTVID: Towards an Open IoT-Platform for Infective Pandemic Diseases such as COVID-19. Sensors (Basel) 2021; 21:E484. [PMID: 33445499 PMCID: PMC7827168 DOI: 10.3390/s21020484] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 12/01/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/22/2022]
Abstract
The factors affecting the penetration of certain diseases such as COVID-19 in society are still unknown. Internet of Things (IoT) technologies can play a crucial role during the time of crisis and they can provide a more holistic view of the reasons that govern the outbreak of a contagious disease. The understanding of COVID-19 will be enriched by the analysis of data related to the phenomena, and this data can be collected using IoT sensors. In this paper, we show an integrated solution based on IoT technologies that can serve as opportunistic health data acquisition agents for combating the pandemic of COVID-19, named CIoTVID. The platform is composed of four layers-data acquisition, data aggregation, machine intelligence and services, within the solution. To demonstrate its validity, the solution has been tested with a use case based on creating a classifier of medical conditions using real data of voice, performing successfully. The layer of data aggregation is particularly relevant in this kind of solution as the data coming from medical devices has a very different nature to that coming from electronic sensors. Due to the adaptability of the platform to heterogeneous data and volumes of data; individuals, policymakers, and clinics could benefit from it to fight the propagation of the pandemic.
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Rodríguez-Galán O, García-Gómez JJ, Rosado IV, Wei W, Méndez-Godoy A, Pillet B, Alekseenko A, Steinmetz L, Pelechano V, Kressler D, de la Cruz J. A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Nucleic Acids Res 2021; 49:206-220. [PMID: 33330942 PMCID: PMC7797049 DOI: 10.1093/nar/gkaa1200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/19/2020] [Revised: 11/18/2020] [Accepted: 12/14/2020] [Indexed: 12/03/2022] Open
Abstract
Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5' region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.
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Affiliation(s)
- Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Juan J García-Gómez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Iván V Rosado
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Alfonso Méndez-Godoy
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, School of Medicine, Stanford, CA, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
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Stepanova D, Byrne HM, Maini PK, Alarcón T. A multiscale model of complex endothelial cell dynamics in early angiogenesis. PLoS Comput Biol 2021; 17:e1008055. [PMID: 33411727 PMCID: PMC7817011 DOI: 10.1371/journal.pcbi.1008055] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/20/2021] [Accepted: 11/19/2020] [Indexed: 12/30/2022] Open
Abstract
We introduce a hybrid two-dimensional multiscale model of angiogenesis, the process by which endothelial cells (ECs) migrate from a pre-existing vascular bed in response to local environmental cues and cell-cell interactions, to create a new vascular network. Recent experimental studies have highlighted a central role of cell rearrangements in the formation of angiogenic networks. Our model accounts for this phenomenon via the heterogeneous response of ECs to their microenvironment. These cell rearrangements, in turn, dynamically remodel the local environment. The model reproduces characteristic features of angiogenic sprouting that include branching, chemotactic sensitivity, the brush border effect, and cell mixing. These properties, rather than being hardwired into the model, emerge naturally from the gene expression patterns of individual cells. After calibrating and validating our model against experimental data, we use it to predict how the structure of the vascular network changes as the baseline gene expression levels of the VEGF-Delta-Notch pathway, and the composition of the extracellular environment, vary. In order to investigate the impact of cell rearrangements on the vascular network structure, we introduce the mixing measure, a scalar metric that quantifies cell mixing as the vascular network grows. We calculate the mixing measure for the simulated vascular networks generated by ECs of different lineages (wild type cells and mutant cells with impaired expression of a specific receptor). Our results show that the time evolution of the mixing measure is directly correlated to the generic features of the vascular branching pattern, thus, supporting the hypothesis that cell rearrangements play an essential role in sprouting angiogenesis. Furthermore, we predict that lower cell rearrangement leads to an imbalance between branching and sprout elongation. Since the computation of this statistic requires only individual cell trajectories, it can be computed for networks generated in biological experiments, making it a potential biomarker for pathological angiogenesis. Angiogenesis, the process by which new blood vessels are formed by sprouting from the pre-existing vascular bed, plays a key role in both physiological and pathological processes, including tumour growth. The structure of a growing vascular network is determined by the coordinated behaviour of endothelial cells in response to various signalling cues. Recent experimental studies have highlighted the importance of cell rearrangements as a driver for sprout elongation. However, the functional role of this phenomenon remains unclear. We formulate a new multiscale model of angiogenesis which, by accounting explicitly for the complex dynamics of endothelial cells within growing angiogenic sprouts, is able to reproduce generic features of angiogenic structures (branching, chemotactic sensitivity, cell mixing, etc.) as emergent properties of its dynamics. We validate our model against experimental data and then use it to quantify the phenomenon of cell mixing in vascular networks generated by endothelial cells of different lineages. Our results show that there is a direct correlation between the time evolution of cell mixing in a growing vascular network and its branching structure, thus paving the way for understanding the functional role of cell rearrangements in angiogenesis.
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Affiliation(s)
- Daria Stepanova
- Centre de Recerca Matemàtica, Bellaterra (Barcelona), Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- * E-mail:
| | - Helen M. Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Tomás Alarcón
- Centre de Recerca Matemàtica, Bellaterra (Barcelona), Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Barcelona, Spain
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Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K. DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. PLoS Comput Biol 2021; 17:e1008551. [PMID: 33481784 PMCID: PMC7857587 DOI: 10.1371/journal.pcbi.1008551] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 08/18/2020] [Revised: 02/03/2021] [Accepted: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
Owing to their plasticity, intrinsically disordered and multidomain proteins require descriptions based on multiple conformations, thus calling for techniques and analysis tools that are capable of dealing with conformational ensembles rather than a single protein structure. Here, we introduce DEER-PREdict, a software program to predict Double Electron-Electron Resonance distance distributions as well as Paramagnetic Relaxation Enhancement rates from ensembles of protein conformations. DEER-PREdict uses an established rotamer library approach to describe the paramagnetic probes which are bound covalently to the protein.DEER-PREdict has been designed to operate efficiently on large conformational ensembles, such as those generated by molecular dynamics simulation, to facilitate the validation or refinement of molecular models as well as the interpretation of experimental data. The performance and accuracy of the software is demonstrated with experimentally characterized protein systems: HIV-1 protease, T4 Lysozyme and Acyl-CoA-binding protein. DEER-PREdict is open source (GPLv3) and available at github.com/KULL-Centre/DEERpredict and as a Python PyPI package pypi.org/project/DEERPREdict.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - João M. Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ramon Crehuet
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), Barcelona, Spain
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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