1
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Afonin DA, Gerasimov ES, Škodová-Sveráková I, Záhonová K, Gahura O, Albanaz ATS, Myšková E, Bykova A, Paris Z, Lukeš J, Opperdoes FR, Horváth A, Zimmer SL, Yurchenko V. Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucleic Acids Res 2024; 52:3870-3885. [PMID: 38452217 DOI: 10.1093/nar/gkae168] [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: 06/20/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The canonical stop codons of the nuclear genome of the trypanosomatid Blastocrithidia nonstop are recoded. Here, we investigated the effect of this recoding on the mitochondrial genome and gene expression. Trypanosomatids possess a single mitochondrion and protein-coding transcripts of this genome require RNA editing in order to generate open reading frames of many transcripts encoded as 'cryptogenes'. Small RNAs that can number in the hundreds direct editing and produce a mitochondrial transcriptome of unusual complexity. We find B. nonstop to have a typical trypanosomatid mitochondrial genetic code, which presumably requires the mitochondrion to disable utilization of the two nucleus-encoded suppressor tRNAs, which appear to be imported into the organelle. Alterations of the protein factors responsible for mRNA editing were also documented, but they have likely originated from sources other than B. nonstop nuclear genome recoding. The population of guide RNAs directing editing is minimal, yet virtually all genes for the plethora of known editing factors are still present. Most intriguingly, despite lacking complex I cryptogene guide RNAs, these cryptogene transcripts are stochastically edited to high levels.
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MESH Headings
- Genome, Mitochondrial
- RNA Editing
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Open Reading Frames/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Trypanosomatina/genetics
- Trypanosomatina/metabolism
- Codon/genetics
- Mitochondria/genetics
- Mitochondria/metabolism
- Codon, Terminator/genetics
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- Genetic Code
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
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Affiliation(s)
- Dmitry A Afonin
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Evgeny S Gerasimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV 252 50 Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, T6G 2R3 Edmonton, Alberta, Canada
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Eva Myšková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Fred R Opperdoes
- De Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Sara L Zimmer
- University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
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2
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de Moura TR, Purta E, Bernat A, Martín-Cuevas E, Kurkowska M, Baulin E, Mukherjee S, Nowak J, Biela A, Rawski M, Glatt S, Moreno-Herrero F, Bujnicki J. Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Nucleic Acids Res 2024; 52:3419-3432. [PMID: 38426934 PMCID: PMC11014237 DOI: 10.1093/nar/gkae144] [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: 10/09/2023] [Revised: 01/25/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes, in particular the 5'-proximal region, which is pivotal for viral protein synthesis. Using a combination of cryo-electron microscopy, atomic force microscopy, chemical probing, and computational modeling, we determined the structures of 5'-proximal regions in RNA genomes of Betacoronaviruses from four subgenera: OC43-CoV, SARS-CoV-2, MERS-CoV, and Rousettus bat-CoV. We obtained cryo-electron microscopy maps and determined atomic-resolution models for the stem-loop-5 (SL5) region at the translation start site and found that despite low sequence similarity and variable length of the helical elements it exhibits a remarkable structural conservation. Atomic force microscopy imaging revealed a common domain organization and a dynamic arrangement of structural elements connected with flexible linkers across all four Betacoronavirus subgenera. Together, these results reveal common features of a critical regulatory region shared between different Betacoronavirus RNA genomes, which may allow targeting of these RNAs by broad-spectrum antiviral therapeutics.
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Affiliation(s)
- Tales Rocha de Moura
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Elżbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Agata Bernat
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Eva M Martín-Cuevas
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Małgorzata Kurkowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Eugene F Baulin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Jakub Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur P Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
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3
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Molinero E, Pena RN, Estany J, Ros-Freixedes R. A novel QTL region for pH and meat color in Duroc pigs. Anim Genet 2024. [PMID: 38584305 DOI: 10.1111/age.13426] [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: 03/21/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
One of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional candidate genes in these regions included PRKAG3 and PHKG1. The SSC8 region, at 71.6 Mb, was novel and, although no candidate causative gene could be identified, it may have regulatory effects. Subsequent analysis on 828 pigs from the same population confirmed the impact of the three associated regions on pH and meat color. We detected no interaction between the three regions. Further investigations are necessary to unravel the functional significance of the novel genomic region at SSC8. These variants could be used as markers in marker-assisted selection for improving meat quality.
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Affiliation(s)
- Eduard Molinero
- Departament de Ciència Animal, Universitat de Lleida, Lleida, Spain
- Agrotecnio-CERCA Center, Lleida, Spain
| | - Ramona N Pena
- Departament de Ciència Animal, Universitat de Lleida, Lleida, Spain
- Agrotecnio-CERCA Center, Lleida, Spain
| | - Joan Estany
- Departament de Ciència Animal, Universitat de Lleida, Lleida, Spain
- Agrotecnio-CERCA Center, Lleida, Spain
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida, Lleida, Spain
- Agrotecnio-CERCA Center, Lleida, Spain
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Bobrovs R, Bolsakova J, Buitrago JAR, Varaceva L, Skvorcova M, Kanepe I, Rudnickiha A, Parisini E, Jirgensons A. Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors. PLoS One 2024; 19:e0296995. [PMID: 38558084 PMCID: PMC10984466 DOI: 10.1371/journal.pone.0296995] [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: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024] Open
Abstract
Emerging resistance to existing antimalarial drugs drives the search for new antimalarials, and protein translation is a promising pathway to target. Threonyl t-RNA synthetase (ThrRS) is one of the enzymes involved in this pathway, and it has been validated as an anti-malarial drug target. Here, we present 9 structurally diverse low micromolar Plasmodium falciparum ThrRS inhibitors that were identified using high-throughput virtual screening (HTVS) and were verified in a FRET enzymatic assay. Salicylic acid-based compound (LE = 0.34) was selected as a most perspective hit and was subjected to hit-to-lead optimisation. A total of 146 hit analogues were synthesised or obtained from commercial vendors and were tested. Structure-activity relationship study was supported by the crystal structure of the complex of a salicylic acid analogue with a close homologue of the plasmodium target, E. coli ThrRS (EcThrRS). Despite the availability of structural information, the hit identified via virtual screening remained one of the most potent PfThrRS inhibitors within this series. However, the compounds presented herein provide novel scaffolds for ThrRS inhibitors, which could serve as starting points for further medicinal chemistry projects targeting ThrRSs or structurally similar enzymes.
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Affiliation(s)
| | | | | | | | | | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Riga, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
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5
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Shang B, Agathokleous E, Calatayud V, Peng J, Xu Y, Li S, Liu S, Feng Z. Drought mitigates the adverse effects of O 3 on plant photosynthesis rather than growth: A global meta-analysis considering plant functional types. Plant Cell Environ 2024; 47:1269-1284. [PMID: 38185874 DOI: 10.1111/pce.14808] [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: 05/16/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Tropospheric ozone (O3 ) is a phytotoxic air pollutant adversely affecting plant growth. High O3 exposures are often concurrent with summer drought. The effects of both stresses on plants are complex, and their interactions are not yet well understood. Here, we investigate whether drought can mitigate the negative effects of O3 on plant physiology and growth based on a meta-analysis. We found that drought mitigated the negative effects of O3 on plant photosynthesis, but the modification of the O3 effect on the whole-plant biomass by drought was not significant. This is explained by a compensatory response of water-deficient plants that leads to increased metabolic costs. Relative to water control condition, reduced water treatment decreased the effects of O3 on photosynthetic traits, and leaf and root biomass in deciduous broadleaf species, while all traits in evergreen coniferous species showed no significant response. This suggested that the mitigating effects of drought on the negative impacts of O3 on the deciduous broadleaf species were more extensive than on the evergreen coniferous ones. Therefore, to avoid over- or underestimations when assessing the impact of O3 on vegetation growth, soil moisture should be considered. These results contribute to a better understanding of terrestrial ecosystem responses under global change.
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Affiliation(s)
- Bo Shang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Evgenios Agathokleous
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Vicent Calatayud
- Fundación CEAM, c/Charles R. Darwin 14, Parque Tecnológico, Paterna, Valencia, Spain
| | - Jinlong Peng
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Yansen Xu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Shuangjiang Li
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Shuo Liu
- Zhejiang Carbon Neutral Innovation Institute, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Zhaozhong Feng
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
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6
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Fernández-González J, Haquin B, Combes E, Bernard K, Allard A, Isidro Y Sánchez J. Maximizing efficiency in sunflower breeding through historical data optimization. Plant Methods 2024; 20:42. [PMID: 38493115 PMCID: PMC10943787 DOI: 10.1186/s13007-024-01151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/30/2024] [Indexed: 03/18/2024]
Abstract
Genomic selection (GS) has become an increasingly popular tool in plant breeding programs, propelled by declining genotyping costs, an increase in computational power, and rediscovery of the best linear unbiased prediction methodology over the past two decades. This development has led to an accumulation of extensive historical datasets with genotypic and phenotypic information, triggering the question of how to best utilize these datasets. Here, we investigate whether all available data or a subset should be used to calibrate GS models for across-year predictions in a 7-year dataset of a commercial hybrid sunflower breeding program. We employed a multi-objective optimization approach to determine the ideal years to include in the training set (TRS). Next, for a given combination of TRS years, we further optimized the TRS size and its genetic composition. We developed the Min_GRM size optimization method which consistently found the optimal TRS size, reducing dimensionality by 20% with an approximately 1% loss in predictive ability. Additionally, the Tails_GEGVs algorithm displayed potential, outperforming the use of all data by using just 60% of it for grain yield, a high-complexity, low-heritability trait. Moreover, maximizing the genetic diversity of the TRS resulted in a consistent predictive ability across the entire range of genotypic values in the test set. Interestingly, the Tails_GEGVs algorithm, due to its ability to leverage heterogeneity, enhanced predictive performance for key hybrids with extreme genotypic values. Our study provides new insights into the optimal utilization of historical data in plant breeding programs, resulting in improved GS model predictive ability.
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Affiliation(s)
- Javier Fernández-González
- Centro de Biotecnologia y Genómica de Plantas (CBGP, UPM-INIA)-Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, Madrid, 28223, Spain.
| | | | | | | | | | - Julio Isidro Y Sánchez
- Centro de Biotecnologia y Genómica de Plantas (CBGP, UPM-INIA)-Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, Madrid, 28223, Spain.
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7
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Gil MA, Cambra JM, Rodriguez-Martinez H, Cuello C, Parrilla I, Martinez EA. In-depth proteome characterization of endometrium and extraembryonic membranes during implantation in pig. J Anim Sci Biotechnol 2024; 15:43. [PMID: 38468318 DOI: 10.1186/s40104-024-01002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/24/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Proteome characterization of the porcine endometrium and extraembryonic membranes is important to understand mother-embryo cross-communication. In this study, the proteome of the endometrium and chorioallantoic membrane was characterized in pregnant sows (PS) during early gestation (d 18 and 24 of gestation) and in the endometrium of non-pregnant sows (NPS) during the same days using LC-MS/MS analysis. The UniProtKB database and ClueGO were used to obtain functional Gene Ontology annotations and biological and functional networks, respectively. RESULTS Our analysis yielded 3,254 and 3,457 proteins identified in the endometrium of PS and NPS, respectively; of these, 1,753 being common while 1,501 and 1,704 were exclusive to PS and NPS, respectively. In addition, we identified 3,968 proteins in the extraembryonic membranes of PS. Further analyses of function revealed some proteins had relevance for the immune system process and biological adhesion in endometrium while the embryonic chorion displayed abundance of proteins related to cell adhesion and cytoskeletal organization, suggesting they dominated the moment of endometrial remodeling, implantation and adhesion of the lining epithelia. Data are available via ProteomeXchange with identifier PXD042565. CONCLUSION This is the first in-depth proteomic characterization of the endometrium and extraembryonic membranes during weeks 3 to 4 of gestation; data that contribute to the molecular understanding of the dynamic environment during this critical period, associated with the majority of pregnancy losses.
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Affiliation(s)
- Maria A Gil
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain
| | | | - Heriberto Rodriguez-Martinez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynaecology, Linköping University, Linköping, Sweden
| | - Cristina Cuello
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain
| | - Inmaculada Parrilla
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain.
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain.
| | - Emilio A Martinez
- Department of Medicine and Animal Surgery, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Pascual Parrilla), Murcia, Spain
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8
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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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9
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Berna-Erro A, Granados MP, Teruel-Montoya R, Ferrer-Marin F, Delgado E, Corbacho AJ, Fenández E, Vazquez-Godoy MT, Tapia JA, Redondo PC. SARAF overexpression impairs thrombin-induced Ca 2+ homeostasis in neonatal platelets. Br J Haematol 2024; 204:988-1004. [PMID: 38062782 DOI: 10.1111/bjh.19210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 03/14/2024]
Abstract
Neonatal platelets present a reduced response to the platelet agonist, thrombin (Thr), thus resulting in a deficient Thr-induced aggregation. These alterations are more pronounced in premature newborns. Here, our aim was to uncover the causes underneath the impaired Ca2+ homeostasis described in neonatal platelets. Both Ca2+ mobilization and Ca2+ influx in response to Thr are decreased in neonatal platelets compared to maternal and control woman platelets. In neonatal platelets, we observed impaired Ca2+ mobilization in response to the PAR-1 agonist (SFLLRN) or by blocking SERCA3 function with tert-butylhydroquinone. Regarding SOCE, the STIM1 regulatory protein, SARAF, was found overexpressed in neonatal platelets, promoting an increase in STIM1/SARAF interaction even under resting conditions. Additionally, higher interaction between SARAF and PDCD61/ALG2 was also observed, reducing SARAF ubiquitination and prolonging its half-life. These results were reproduced by overexpressing SARAF in MEG01 and DAMI cells. Finally, we also observed that pannexin 1 permeability is enhanced in response to Thr in control woman and maternal platelets, but not in neonatal platelets, hence, leading to the deregulation of the Ca2+ entry found in neonatal platelets. Summarizing, we show that in neonatal platelets both Ca2+ accumulation in the intracellular stores and Thr-evoked Ca2+ entry through either capacitative channels or non-selective channels are altered in neonatal platelets, contributing to deregulated Ca2+ homeostasis in neonatal platelets and leading to the altered aggregation observed in these subjects.
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Affiliation(s)
- Alejandro Berna-Erro
- Department of Physiology (PHYCELL Group), University of Extremadura, Caceres, Spain
| | - Maria P Granados
- Pharmacy Unit of Health Center, Extremadura County Health Service, Caceres, Spain
| | - Raul Teruel-Montoya
- Hemodonation County Center, University Hospital of Morales-Meseguer, IMIB-Arrixaca, CIBERER CB55, Murcia, Spain
| | - Francisca Ferrer-Marin
- Hemodonation County Center, University Hospital of Morales-Meseguer, IMIB-Arrixaca, CIBERER CB55, Murcia, Spain
| | - Elena Delgado
- Blood Donation Center, Extremadura County Health Service, Merida, Spain
| | | | | | | | - Jose A Tapia
- Department of Physiology (PHYCELL Group), University of Extremadura, Caceres, Spain
| | - Pedro Cosme Redondo
- Department of Physiology (PHYCELL Group), University of Extremadura, Caceres, Spain
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10
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Bourgeois Y, Warren BH, Augiron S. The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi. Mol Ecol 2024; 33:e17300. [PMID: 38372440 DOI: 10.1111/mec.17300] [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: 08/09/2022] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Anthropogenic impact is causing the decline of a large proportion of species worldwide and reduces their genetic diversity. Island species typically have smaller ranges than continental species. As a consequence, island species are particularly liable to undergo population bottlenecks, giving rise to conservation challenges such as inbreeding and unmasking of deleterious genetic load. Such challenges call for more detailed assessments of the genetic make-up of threatened island populations. The Mascarene islands (Indian Ocean) present many prime examples, being unusual in having been pristine until first human arrival ~400 years ago, following which anthropogenic pressure was unusually intense. A threatened harrier (Circus maillardi) endemic to the westernmost island of the archipelago is a good example of the challenges faced by species that have declined to small population size following intense anthropogenic pressure. In this study, we use an extensive set of population genomic tools to quantify variation at near-neutral and coding loci, in order to test the historical impact of human activity on this species, and evaluate the species' (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants but is unlikely to have allowed the purging of mildly deleterious variants. Our study shows how using relatively affordable methods can reveal the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.
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Affiliation(s)
- Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Steve Augiron
- Société d'Études Ornithologiques de La Réunion, Saint-André, France
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11
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Fernández I, Larrán AM, de Paz P, Riesco MF. The Direct Effects of Climate Change on Tench ( Tinca tinca) Sperm Quality under a Real Heatwave Event Scenario. Animals (Basel) 2024; 14:778. [PMID: 38473163 DOI: 10.3390/ani14050778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Global aquaculture growth will most probably face specific conditions derived from climate change. In fact, the most severe impacts of these changes will be suffered by aquatic populations in restrictive circumstances, such as current aquaculture locations, which represent a perfect model to study global warming effects. Although the impact of temperature on fish reproduction has been characterized in many aspects, this study was focused on recreating more realistic models of global warming, particularly considering heatwave phenomena, in order to decipher its effects on male gametes (spermatozoa). For this purpose, thermal stress via a heatwave simulation (mimicking a natural occurring heatwave, from 24 to 30 °C) was induced in adult tench (Tinca tinca) males and compared with a control group (55.02 ± 16.44 g of average body wet weight). The impact of the thermal stress induced by this climate change event was assessed using cellular and molecular approaches. After the heatwave recreation, a multiparametric analysis of sperm quality, including some traditional parameters (such as sperm motility) and new ones (focus on redox balance and sperm quality biomarkers), was performed. Although sperm concentration and the volume produced were not affected, the results showed a significant deleterious effect on motility parameters (e.g., reduced progressive motility and total motility during the first minute post-activation). Furthermore, the sperm produced under the thermal stress induced by this heatwave simulation exhibited an increased ROS content in spermatic cells, confirming the negative effect that this thermal stress model (heatwave recreation) might have had on sperm quality. More importantly, the expression of some known sperm quality and fertilization markers was decreased in males exposed to thermal stress. This present study not only unveils the potential effects of climate change in contemporary and future fish farming populations (and their underlying mechanisms) but also provides insights on how to mitigate and/or avoid thermal stress due to heatwave events.
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Affiliation(s)
- Ignacio Fernández
- Spanish Institute of Oceanography (IEO-CSIC), Centro Oceanográfico de Vigo, Subida a Radio Faro nº 52, 36390 Vigo, Spain
| | - Ana M Larrán
- Aquaculture Research Center, Agro-Technological Institute of Castilla y León (ITACyL), Ctra. Arévalo, Zamarramala, 40196 Segovia, Spain
| | - Paulino de Paz
- Cell Biology Area, Department of Molecular Biology, Universidad de León, Campus de Vegazana, sn, 24071 León, Spain
| | - Marta F Riesco
- Cell Biology Area, Department of Molecular Biology, Universidad de León, Campus de Vegazana, sn, 24071 León, Spain
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12
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Motevalizadeh E, Díaz-López A, Martín F, Basora J, Arija V. Association of Parity With Insulin Resistance Early in Pregnant Women: ECLIPSES Study. J Clin Endocrinol Metab 2024; 109:730-739. [PMID: 37804535 DOI: 10.1210/clinem/dgad594] [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: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023]
Abstract
CONTEXT Little is known about whether parity is associated with elevated early-pregnancy insulin resistance (IR), or whether overweight/obesity contributes to increasing the possible effect. OBJECTIVE We determined the associations between parity and glucose metabolism parameters in the first trimester of pregnancy in a Mediterranean pregnant population, and whether these associations are affected by overweight/obesity. METHODS A cross-sectional study was conducted of 264 healthy pregnant women from the ECLIPSES study who were recruited at 12 weeks of gestation. At baseline, details on socioeconomic status, obstetric history (including parity, ie, number of births), lifestyle factors, anthropometry, and blood samples were collected. Fasting serum glucose, insulin, and homeostasis model assessment of insulin resistance (HOMA-IR) index were assessed in the first trimester. Elevated IR was defined as the upper HOMA-IR tertile (≥1.58). Multivariable linear regression and Cox regression model with constant time were performed. RESULTS Parity ranged from 0 to 4. After multivariable adjustment, the insulin levels (β [% change]: 20.92; 95% CI, 4.08-37.71) and HOMA-IR index (β [% change]: 19.72; 95% CI, 2.43-40.49) were positively associated with parity. Additionally, multiparous women, as compared to nulliparous, were more likely to have higher HOMA-IR levels (primiparous [1 birth], β [% change[: 16.88; 95% CI, -1.00 to 37.99; multiparous [≥2 births), β [% change]: 32.18; 95% CI, 3.56-68.71), and an increased relative risk (RR) of an elevated IR (primiparous [1 birth], RR: 1.55; 95% CI, 1.03-2.36; multiparous (≥2 births), RR: 1.72; 95% CI, 1.05-2.83). The combination of multiparity and overweight/obesity conferred a 3.04-fold increase in the RR of elevated IR, which increased proportionally to the number of parities. CONCLUSION This study demonstrates that parity may have a negative effect on early-pregnancy IR and that maternal overweight/obesity appears to further aggravate this relationship.
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Affiliation(s)
- Ehsan Motevalizadeh
- Nutrition and Mental Health Research Group (NUTRISAM), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain
| | - Andrés Díaz-López
- Nutrition and Mental Health Research Group (NUTRISAM), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain
- Consorcio CIBER, M.P. Fisiopatología de la Obesidad y la Nutrición (CIBERObn), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Francisco Martín
- Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain
- Institut d'Investigació en Atenció Primària IDIAP Jordi Gol, Institut Català de la Salut (ICS), 08007 Barcelona, Spain
- Collaborative Group on Lifestyles, Nutrition, And Tobacco (CENIT), Institut d'Investigació en Atenció Primària IDIAP Jordi Gol, Institut Català de la Salut (ICS), 43202 Reus, Spain
| | - Josep Basora
- Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain
- Institut d'Investigació en Atenció Primària IDIAP Jordi Gol, Institut Català de la Salut (ICS), 08007 Barcelona, Spain
| | - Victoria Arija
- Nutrition and Mental Health Research Group (NUTRISAM), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain
- Institut d'Investigació en Atenció Primària IDIAP Jordi Gol, Institut Català de la Salut (ICS), 08007 Barcelona, Spain
- Collaborative Group on Lifestyles, Nutrition, And Tobacco (CENIT), Institut d'Investigació en Atenció Primària IDIAP Jordi Gol, Institut Català de la Salut (ICS), 43202 Reus, Spain
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13
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Pereira N, Afonso L, Salado M, Tubio CR, Correia DM, Costa CM, Lanceros-Mendez S. Ionic Thermoelectric Generators in Vertical and Planar Topologies Based on Fluorinated Polymer Hybrid Materials with Ionic Liquids. Macromol Rapid Commun 2024:e2400041. [PMID: 38366845 DOI: 10.1002/marc.202400041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/14/2024] [Indexed: 02/18/2024]
Abstract
Ionic thermoelectrics (TEs), in which voltage generation is based on ion migration, are suitable for applications based on their low cost, high flexibility, high ionic conductivity, and wide range of Seebeck coefficients. This work reports on the development of ionic TE materials based on the poly(vinylidene fluoride-trifluoroethylene), Poly(VDF-co-TrFE), as host polymer blended with different contents of the ionic liquid, IL, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [EMIM][TFSI]. The morphology, physico-chemical, thermal, mechanical, and electrical properties of the samples are evaluated together with the TE response. It is demonstrated that the IL acts as a nucleating agent for polymer crystallization. The mechanical properties and ionic conductivity values are dependent on the IL content. A high room temperature ionic conductivity of 0.008 S cm-1 is obtained for the sample with 60 wt% of [EMIM][TFSI] IL. The TE properties depend on both IL content and device topology-vertical or planar-the largest generated voltage range being obtained for the planar topology and the sample with 10 wt% of IL content, characterized by a Seebeck coefficient of 1.2 mV K-1 . Based on the obtained maximum power density of 4.9 µW m-2 , these materials are suitable for a new generation of TE devices.
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Affiliation(s)
- Nelson Pereira
- Centre of Physics Universities of Minho and Porto and Laboratory of Physics for Materials and Emergent Technologies, LapMET, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Luis Afonso
- Centre of Physics Universities of Minho and Porto and Laboratory of Physics for Materials and Emergent Technologies, LapMET, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Manuel Salado
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, Leioa, 48940, Spain
| | - Carmen R Tubio
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, Leioa, 48940, Spain
| | | | - Carlos M Costa
- Centre of Physics Universities of Minho and Porto and Laboratory of Physics for Materials and Emergent Technologies, LapMET, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Senentxu Lanceros-Mendez
- Centre of Physics Universities of Minho and Porto and Laboratory of Physics for Materials and Emergent Technologies, LapMET, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48009, Spain
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14
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Torvinen P, Ruotsalainen KS, Zhao S, Cronin N, Ohtonen O, Linnamo V. Evaluation of 3D Markerless Motion Capture System Accuracy during Skate Skiing on a Treadmill. Bioengineering (Basel) 2024; 11:136. [PMID: 38391622 PMCID: PMC10886413 DOI: 10.3390/bioengineering11020136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
In this study, we developed a deep learning-based 3D markerless motion capture system for skate skiing on a treadmill and evaluated its accuracy against marker-based motion capture during G1 and G3 skating techniques. Participants performed roller skiing trials on a skiing treadmill. Trials were recorded with two synchronized video cameras (100 Hz). We then trained a custom model using DeepLabCut, and the skiing movements were analyzed using both DeepLabCut-based markerless motion capture and marker-based motion capture systems. We statistically compared joint centers and joint vector angles between the methods. The results demonstrated a high level of agreement for joint vector angles, with mean differences ranging from -2.47° to 3.69°. For joint center positions and toe placements, mean differences ranged from 24.0 to 40.8 mm. This level of accuracy suggests that our markerless approach could be useful as a skiing coaching tool. The method presents interesting opportunities for capturing and extracting value from large amounts of data without the need for markers attached to the skier and expensive cameras.
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Affiliation(s)
- Petra Torvinen
- Faculty of Sport and Health Sciences, University of Jyväskylä, 88610 Jyväskylä, Finland
| | - Keijo S Ruotsalainen
- Faculty of Sport and Health Sciences, University of Jyväskylä, 88610 Jyväskylä, Finland
| | - Shuang Zhao
- Faculty of Sport and Health Sciences, University of Jyväskylä, 88610 Jyväskylä, Finland
| | - Neil Cronin
- Faculty of Sport and Health Sciences, University of Jyväskylä, 88610 Jyväskylä, Finland
| | - Olli Ohtonen
- Faculty of Sport and Health Sciences, University of Jyväskylä, 88610 Jyväskylä, Finland
| | - Vesa Linnamo
- Faculty of Sport and Health Sciences, University of Jyväskylä, 88610 Jyväskylä, Finland
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15
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Glaskova-Kuzmina T, Dejus D, Jātnieks J, Vīndedze E, Bute I, Sevcenko J, Aniskevich A, Stankevich S, Boobani B. The Tensile, Thermal and Flame-Retardant Properties of Polyetherimide and Polyetherketoneketone Processed via Fused Filament Fabrication. Polymers (Basel) 2024; 16:336. [PMID: 38337225 DOI: 10.3390/polym16030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Polymer materials are increasingly widely used in high-fire-risk applications, such as aviation interior components. This study aimed to compare the tensile, thermal, and flame-retardant properties of test samples made from ultra-performance materials, polyetherimide (PEI) and polyetherketoneketone (PEKK), using the fused filament fabrication process (FFF). The tensile tests were performed for these materials at different raster angles (0, 45, and 90°). The thermomechanical tests were done in the axial, perpendicular, and through-thickness directions to the extruded filaments. The impact of printing parameters on the flame retardancy of 3D-printed samples was investigated in vertical burn tests with varying specimen thicknesses and printing directions. Experimentally, it was testified that PEKK had better isotropic behaviour than PEI for mechanical performance, thermal expansion, and fire-resistant properties, which are essential in fabricating intricately shaped products.
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Affiliation(s)
- Tatjana Glaskova-Kuzmina
- Baltic3D.eu, Braslas 22D, LV-1035 Riga, Latvia
- Institute for Mechanics of Materials, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia
| | | | | | | | - Irina Bute
- Institute for Mechanics of Materials, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia
| | - Jevgenijs Sevcenko
- Institute for Mechanics of Materials, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia
| | - Andrey Aniskevich
- Institute for Mechanics of Materials, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia
| | - Stanislav Stankevich
- Institute for Mechanics of Materials, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia
| | - Behnam Boobani
- Latvian Academy of Sport Education, Brivibas 333, LV-1006 Riga, Latvia
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16
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Kulovic-Sissawo A, Tocantins C, Diniz MS, Weiss E, Steiner A, Tokic S, Madreiter-Sokolowski CT, Pereira SP, Hiden U. Mitochondrial Dysfunction in Endothelial Progenitor Cells: Unraveling Insights from Vascular Endothelial Cells. Biology (Basel) 2024; 13:70. [PMID: 38392289 PMCID: PMC10886154 DOI: 10.3390/biology13020070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024]
Abstract
Endothelial dysfunction is associated with several lifestyle-related diseases, including cardiovascular and neurodegenerative diseases, and it contributes significantly to the global health burden. Recent research indicates a link between cardiovascular risk factors (CVRFs), excessive production of reactive oxygen species (ROS), mitochondrial impairment, and endothelial dysfunction. Circulating endothelial progenitor cells (EPCs) are recruited into the vessel wall to maintain appropriate endothelial function, repair, and angiogenesis. After attachment, EPCs differentiate into mature endothelial cells (ECs). Like ECs, EPCs are also susceptible to CVRFs, including metabolic dysfunction and chronic inflammation. Therefore, mitochondrial dysfunction of EPCs may have long-term effects on the function of the mature ECs into which EPCs differentiate, particularly in the presence of endothelial damage. However, a link between CVRFs and impaired mitochondrial function in EPCs has hardly been investigated. In this review, we aim to consolidate existing knowledge on the development of mitochondrial and endothelial dysfunction in the vascular endothelium, place it in the context of recent studies investigating the consequences of CVRFs on EPCs, and discuss the role of mitochondrial dysfunction. Thus, we aim to gain a comprehensive understanding of mechanisms involved in EPC deterioration in relation to CVRFs and address potential therapeutic interventions targeting mitochondrial health to promote endothelial function.
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Affiliation(s)
- Azra Kulovic-Sissawo
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Carolina Tocantins
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- CNC-UC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-504 Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-531 Coimbra, Portugal
| | - Mariana S Diniz
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- CNC-UC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-504 Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-531 Coimbra, Portugal
| | - Elisa Weiss
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Andreas Steiner
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Silvija Tokic
- Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
| | - Corina T Madreiter-Sokolowski
- Division of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Susana P Pereira
- CNC-UC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-504 Coimbra, Portugal
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, 4200-450 Porto, Portugal
| | - Ursula Hiden
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
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17
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Palomino-Cabrera R, Tejerina F, Molero-Salinas A, Veintimilla C, Catalán P, Ferris M, Osorio S, Alonso R, Muñoz P, de García de Viedma D, Pérez-Lago L. No emergence of resistance mutations in COVID-19 patients receiving nirmatrelvir/ritonavir. J Med Virol 2024; 96:e29337. [PMID: 38149407 DOI: 10.1002/jmv.29337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Affiliation(s)
- Rosalía Palomino-Cabrera
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Francisco Tejerina
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas-CIBERINFEC, Madrid, Spain
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María Ferris
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Farmacia, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Santiago Osorio
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Hematología, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, Madrid, Spain
| | - Darío de García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
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18
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D’Arrigo M, Delgado-Adámez J, Rocha-Pimienta J, Valdés-Sánchez ME, Ramírez-Bernabé MR. Integral Use of Red Wine Pomace after Hydrostatic High Pressure: Application of Two Consecutive Cycles of Treatment. Foods 2024; 13:149. [PMID: 38201177 PMCID: PMC10778647 DOI: 10.3390/foods13010149] [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: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The influence of applying hydrostatic high pressure (HHP) to red grape pomace cv. Tempranillo was studied to obtain an ingredient rich in bioactive compounds for the manufacture of food products. Four treatments were investigated: (i) 600 MPa/1 s; (ii) 600 MPa/300 s, and other two treatments with 2 cycles of HHP: (iii) 2 cycles of 600 MPa/1 s; and (iv) 1 first cycle of 400 MPa/1 s and a second cycle 600 MPa/1 s. Treated pomace was stored at different temperatures (4 and 20 °C). The application of two consecutive cycles had no effect on the microorganisms' inactivation compared to only one cycle. Immediately after HHP, the phenolic compounds content was maintained. However, HHP had no influence on the polyphenol oxidase enzyme (PPO), and so the phenolic compounds were significantly reduced during storage. Hence, the shelf-life of red grape pomace was significantly reduced at both temperatures, although phenolic compounds were better preserved under refrigeration than at room temperature.
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Affiliation(s)
| | | | | | | | - M. Rosario Ramírez-Bernabé
- Technological Agri-Food Institute (INTAEX), Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Avda Adolfo Suárez s/n, 06071 Badajoz, Spain; (M.D.); (J.D.-A.); (J.R.-P.); (M.E.V.-S.)
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19
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Kirpluks M, Abolins A, Eihe D, Pomilovskis R, Fridrihsone A. Rapeseed Oil as Feedstock for Bio-Based Thermoset Foams Obtained via Michael Addition Reaction. Polymers (Basel) 2023; 16:117. [PMID: 38201783 PMCID: PMC10780781 DOI: 10.3390/polym16010117] [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: 11/27/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Rapeseed oil was used to develop thermoset foams via Michael addition reaction by mixing two liquid components, Michael donor and Michael acceptor. The foaming of the curing thermoset was achieved by the physical blowing agent which expanded from the reacting foam mass due to an exothermic curing reaction. The influence of the rapeseed oil-based Michael donor functionality on the foaming process and the characteristics of the obtained thermoset foams was studied. The 1,1,3,3-tetramethylguanidine catalyst's influence on the foaming process kinetics was studied using FOAMAT equipment. The curing of the bio-based thermoset was analysed using a dielectric polarisation sensor. The morphology of the developed thermoset foam was analysed using a scanning electron microscope and the obtained foams were characterized using TGA, DSC, DMA and mechanical analysis tests. A direct correlation between the thermoset foam polymer crosslinking density and foaming reactivity, mechanical properties and glass transition temperature were determined. Obtained rapeseed oil based thermoset foams had a relatively low thermal conductivity of 33.9-35.4 mW/(m·K) which allows their use as thermal insulation material in civil engineering applications.
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Affiliation(s)
- Mikelis Kirpluks
- Polymer Laboratory, Latvian State Institute of Wood Chemistry, Str. Dzerbenes 27, LV-1006 Riga, Latvia; (A.A.); (D.E.); (R.P.); (A.F.)
| | - Arnis Abolins
- Polymer Laboratory, Latvian State Institute of Wood Chemistry, Str. Dzerbenes 27, LV-1006 Riga, Latvia; (A.A.); (D.E.); (R.P.); (A.F.)
| | - Darta Eihe
- Polymer Laboratory, Latvian State Institute of Wood Chemistry, Str. Dzerbenes 27, LV-1006 Riga, Latvia; (A.A.); (D.E.); (R.P.); (A.F.)
| | - Ralfs Pomilovskis
- Polymer Laboratory, Latvian State Institute of Wood Chemistry, Str. Dzerbenes 27, LV-1006 Riga, Latvia; (A.A.); (D.E.); (R.P.); (A.F.)
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Str. P. Valdena 3/7, LV-1048 Riga, Latvia
| | - Anda Fridrihsone
- Polymer Laboratory, Latvian State Institute of Wood Chemistry, Str. Dzerbenes 27, LV-1006 Riga, Latvia; (A.A.); (D.E.); (R.P.); (A.F.)
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20
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Vega M, Barrios R, Fraile R, de Castro Cogle K, Castillo D, Anglada R, Casals F, Ayté J, Lowy-Gallego E, Hidalgo E. Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery. Nucleic Acids Res 2023; 51:12161-12173. [PMID: 37956308 PMCID: PMC10711424 DOI: 10.1093/nar/gkad1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin remodeling is essential to allow full development of alternative gene expression programs in response to environmental changes. In fission yeast, oxidative stress triggers massive transcriptional changes including the activation of hundreds of genes, with the participation of histone modifying complexes and chromatin remodelers. DNA transcription is associated to alterations in DNA topology, and DNA topoisomerases facilitate elongation along gene bodies. Here, we test whether the DNA topoisomerase Top1 participates in the RNA polymerase II-dependent activation of the cellular response to oxidative stress. Cells lacking Top1 are resistant to H2O2 stress. The transcriptome of Δtop1 strain was not greatly affected in the absence of stress, but activation of the anti-stress gene expression program was more sustained than in wild-type cells. Top1 associated to stress open reading frames. While the nucleosomes of stress genes are partially and transiently evicted during stress, the chromatin configuration remains open for longer times in cells lacking Top1, facilitating RNA polymerase II progression. We propose that, by removing DNA tension arising from transcription, Top1 facilitates nucleosome reassembly and works in synergy with the chromatin remodeler Hrp1 as opposing forces to transcription and to Snf22 / Hrp3 opening remodelers.
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Affiliation(s)
- Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rubén Barrios
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rodrigo Fraile
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | | | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ernesto Lowy-Gallego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
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21
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Ostrožovičová M, Mecheri Y, Al-Mubarak BR, Al-Tassan N, Makarious MB, Periñan MT, Bandres-Ciga S. PTPA variants and the risk for Parkinson's disease in diverse ancestry populations. Brain 2023; 146:e120-e124. [PMID: 37467482 PMCID: PMC10689897 DOI: 10.1093/brain/awad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Affiliation(s)
- Miriam Ostrožovičová
- Department of Neurology, P.J. Safarik University, Kosice 04011, Slovak Republic
- Department of Neurology, University Hospital of L. Pasteur, Kosice 04011, Slovak Republic
| | - Yasser Mecheri
- Neurology Department, Dr Benbadis University Hospital, Constantine 25018, Algeria
| | - Bashayer R Al-Mubarak
- Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Nada Al-Tassan
- Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- UCL Movement Disorders Centre, University College London, WC1N 3BG London, UK
| | - Maria Teresa Periñan
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Sevilla, 41013 Seville, Spain
- Preventive Neurology Unit, Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, EC1M 6BQ London, UK
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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22
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Hidalgo-Figueroa M, Salazar A, Romero-López-Alberca C, MacDowell KS, García-Bueno B, Bioque M, Bernardo M, Parellada M, González-Pinto A, García-Portilla MP, Lobo A, Rodriguez-Jimenez R, Berrocoso E, Leza JC. Association of Prolactin, Oxytocin, and Homocysteine With the Clinical and Cognitive Features of a First Episode of Psychosis Over a 1-Year Follow-Up. Int J Neuropsychopharmacol 2023; 26:796-807. [PMID: 37603404 PMCID: PMC10674080 DOI: 10.1093/ijnp/pyad051] [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: 04/03/2023] [Accepted: 08/20/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND The clinical debut of schizophrenia is frequently a first episode of psychosis (FEP). As such, there is considerable interest in identifying associations between biological markers and clinical or cognitive characteristics that help predict the progression and outcome of FEP patients. Previous studies showed that high prolactin, low oxytocin, and high homocysteine are factors associated with FEP 6 months after diagnosis, at which point plasma levels were correlated with some clinical and cognitive characteristics. METHODS We reexamined 75 patients at 12 months after diagnosis to measure the evolution of these molecules and assess their association with clinical features. RESULTS At follow-up, FEP patients had lower prolactin levels than at baseline, and patients treated with risperidone or paliperidone had higher prolactin levels than patients who received other antipsychotic agents. By contrast, no changes in oxytocin and homocysteine plasma levels were observed between the baseline and follow-up. In terms of clinical features, we found that plasma prolactin and homocysteine levels were correlated with the severity of the psychotic symptoms in male FEP patients, suggesting that they might be factors associated with psychotic symptomatology but only in men. Together with oxytocin, these molecules may also be related to sustained attention, verbal ability, and working memory cognitive domains in FEP patients. CONCLUSION This study suggests that focusing on prolactin, oxytocin, and homocysteine at a FEP may help select adequate pharmacological treatments and develop new tools to improve the outcome of these patients, where sex should also be borne in mind.
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Affiliation(s)
- Maria Hidalgo-Figueroa
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cádiz, Spain
- Neuropsychopharmacology and Psychobiology Research Group, Psychobiology Area, Department of Psychology, Universidad de Cádiz, Puerto Real (Cádiz), Spain
| | - Alejandro Salazar
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cádiz, Spain
- Department of Statistics and Operational Research, University of Cádiz, Puerto Real (Cádiz), Spain
- The Observatory of Pain, University of Cádiz, Cádiz, Spain
| | - Cristina Romero-López-Alberca
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cádiz, Spain
- Personality, Evaluation and Psychological Treatment Area, Department of Psychology, Universidad de Cádiz, Puerto Real (Cádiz), Spain
| | - Karina S MacDowell
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Departamento de Farmacología y Toxicología, Facultad de Medicina, Univ. Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre (i+12), IUINQ, Madrid, Spain
| | - Borja García-Bueno
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Departamento de Farmacología y Toxicología, Facultad de Medicina, Univ. Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre (i+12), IUINQ, Madrid, Spain
| | - Miquel Bioque
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Institut d’investigacions Biomèdiques August Pi i Sunyer (IDIBAPs), Barcelona Clínic Schizophrenia Unit (BCSU), Neuroscience Institute, Hospital Clínic de Barcelona, Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Miquel Bernardo
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Institut d’investigacions Biomèdiques August Pi i Sunyer (IDIBAPs), Barcelona Clínic Schizophrenia Unit (BCSU), Neuroscience Institute, Hospital Clínic de Barcelona, Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Mara Parellada
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Ana González-Pinto
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Department of Psychiatry, Hospital Universitario de Alava, BIOARABA, EHU, Vitoria-Gasteiz, Spain
| | - M Paz García-Portilla
- Department of Psychiatry, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Neurociencias del Principado de Asturias (INEUROPA), Servicio de Salud del Principado de Asturias (SESPA), Oviedo, Spain
| | - Antonio Lobo
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Department of Medicine and Psychiatry, Universidad de Zaragoza, Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Roberto Rodriguez-Jimenez
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Department of Psychiatry, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12)/Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Esther Berrocoso
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cádiz, Spain
- Neuropsychopharmacology and Psychobiology Research Group, Psychobiology Area, Department of Psychology, Universidad de Cádiz, Puerto Real (Cádiz), Spain
| | - Juan C Leza
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), ISCIII, Madrid, Spain
- Departamento de Farmacología y Toxicología, Facultad de Medicina, Univ. Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre (i+12), IUINQ, Madrid, Spain
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23
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Matejova J, Fecskeova LK, Slovinska L, Harvanova D, Spakova T, Bzdilova J. Plasma-derived extracellular vesicle surface markers CD45, CD326 and CD56 correlate with the stage of osteoarthritis: a primary study of a novel and promising diagnostic tool of the disease. Sci Rep 2023; 13:20071. [PMID: 37973964 PMCID: PMC10654566 DOI: 10.1038/s41598-023-47074-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] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023] Open
Abstract
Recently, there is a growing interest in the research based on extracellular vesicles (EVs) which represent paracrine factors secreted by almost all cell types. Both, normal and pathological cells are able to release various types of EVs with different physiological properties, functions and compositions. EVs play an important role in intercellular communication, mechanism and tissue repair. Moreover, EVs could help not only in the treatment of diseases but also in their diagnostics. This work focused on the evaluation of the potential of EVs being used as biomarkers for the diagnosis of osteoarthritis (OA) based on a comparison of the composition of EVs separated from platelet-poor plasma (PPP) of healthy donors and OA patients at different stages of OA. OA is established as a complex syndrome with extensive impact on multiple tissues within the synovial joint. It is a chronic disease of musculoskeletal system that mainly affects the elderly. Depending on the use of the Kellgren-Lawrence classification system, there are four grades of OA which have a negative impact on patients' quality of life. It is very difficult to detect OA in its early stages, so it is necessary to find a new diagnostic method for its timely detection. PPP samples were prepared from whole blood. PPP-EVs were separated from 3 groups of donors-healthy control, early stage OA, end-stage OA, and their content was compared and correlated. EVs from PPP were separated by size exclusion chromatography and characterized in terms of their size, yield and purity by NTA, western blotting, ELISA and flow cytometry. Detection of surface markers expression in EVs was performed using MACSPlex approach. Inflammatory and growth factors in EVs were analysed using MAGPix technology. Our study confirmed significant differences between EVs surface markers of patients and healthy controls correlating with the age of donor (CD63, CD31 and ROR1) and stage of OA (CD45, CD326 and CD56), respectively. Circulating EVs have been under extensive investigation for their capability to predict OA pathology diagnosis as potential targets for biomarker discovery. Taken together, obtained results indicated that PPP-EVs surface markers could be used as potential biomarkers in the early diagnosis of OA.
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Affiliation(s)
- Jana Matejova
- Associated Tissue Bank, Faculty of Medicine, P. J. Safarik University and L. Pasteur University Hospital in Kosice, Tr. SNP 1, 04011, Kosice, Slovakia
| | - Livia K Fecskeova
- Associated Tissue Bank, Faculty of Medicine, P. J. Safarik University and L. Pasteur University Hospital in Kosice, Tr. SNP 1, 04011, Kosice, Slovakia
| | - Lucia Slovinska
- Associated Tissue Bank, Faculty of Medicine, P. J. Safarik University and L. Pasteur University Hospital in Kosice, Tr. SNP 1, 04011, Kosice, Slovakia
| | - Denisa Harvanova
- Associated Tissue Bank, Faculty of Medicine, P. J. Safarik University and L. Pasteur University Hospital in Kosice, Tr. SNP 1, 04011, Kosice, Slovakia
| | - Timea Spakova
- Associated Tissue Bank, Faculty of Medicine, P. J. Safarik University and L. Pasteur University Hospital in Kosice, Tr. SNP 1, 04011, Kosice, Slovakia
| | - Jana Bzdilova
- Associated Tissue Bank, Faculty of Medicine, P. J. Safarik University and L. Pasteur University Hospital in Kosice, Tr. SNP 1, 04011, Kosice, Slovakia.
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24
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Motamedian E, Berzins K, Muiznieks R, Stalidzans E. OptEnvelope: A target point guided method for growth-coupled production using knockouts. PLoS One 2023; 18:e0294313. [PMID: 37972019 PMCID: PMC10653430 DOI: 10.1371/journal.pone.0294313] [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: 08/04/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a mathematic model of metabolism is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is presented based on finding minimal set of active reactions for a target point in the feasible solution space (envelope) using a mixed-integer linear programming formula. The method initially finds the reduced desirable solution space envelope in the product versus biomass plot by removing all inactive reactions. Then, with reinsertion of the deleted reactions, OptEnvelope attempts to reduce the number of knockouts so that the desirable production envelope is preserved. Additionally, OptEnvelope searches for envelopes with higher minimum production rates or fewer knockouts by evaluating different target points within the desired solution space. It is possible to limit the maximal number of knockouts. The method was implemented on metabolic models of E. coli and S. cerevisiae to test the method benchmarking the capability of these industrial microbes for overproduction of acetate and glycerol under aerobic conditions and succinate and ethanol under anaerobic conditions. The results illustrate that OptEnvelope is capable to find multiple strong coupled envelopes located in the desired solution space because of its novel target point oriented strategy of envelope search. The results indicate that E. coli is more appropriate to produce acetate and succinate while S. cerevisiae is a better host for glycerol production. Gene deletions for some of the proposed reaction knockouts have been previously reported to increase the production of these metabolites in experiments. Both organisms are suitable for ethanol production, however, more knockouts for the adaptation of E. coli are required. OptEnvelope is available at https://github.com/lv-csbg/optEnvelope.
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Affiliation(s)
- Ehsan Motamedian
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Kristaps Berzins
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Reinis Muiznieks
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Egils Stalidzans
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
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25
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Taborska P, Lukac P, Stakheev D, Rajsiglova L, Kalkusova K, Strnadova K, Lacina L, Dvorankova B, Novotny J, Kolar M, Vrana M, Cechova H, Ransdorfova S, Valerianova M, Smetana K, Vannucci L, Smrz D. Novel PD-L1- and collagen-expressing patient-derived cell line of undifferentiated pleomorphic sarcoma (JBT19) as a model for cancer immunotherapy. Sci Rep 2023; 13:19079. [PMID: 37925511 PMCID: PMC10625569 DOI: 10.1038/s41598-023-46305-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
Soft tissue sarcomas are aggressive mesenchymal-origin malignancies. Undifferentiated pleomorphic sarcoma (UPS) belongs to the aggressive, high-grade, and least characterized sarcoma subtype, affecting multiple tissues and metastasizing to many organs. The treatment of localized UPS includes surgery in combination with radiation therapy. Metastatic forms are treated with chemotherapy. Immunotherapy is a promising treatment modality for many cancers. However, the development of immunotherapy for UPS is limited due to its heterogeneity, antigenic landscape variation, lower infiltration with immune cells, and a limited number of established patient-derived UPS cell lines for preclinical research. In this study, we established and characterized a novel patient-derived UPS cell line, JBT19. The JBT19 cells express PD-L1 and collagen, a ligand of the immune checkpoint molecule LAIR-1. JBT19 cells can form spheroids in vitro and solid tumors in immunodeficient nude mice. We found JBT19 cells induce expansion of JBT19-reactive autologous and allogeneic NK, T, and NKT-like cells, and the reactivity of the expanded cells was associated with cytotoxic impact on JBT19 cells. The PD-1 and LAIR-1 ligand-expressing JBT19 cells show ex vivo immunogenicity and effective in vivo xenoengraftment properties that can offer a unique resource in the preclinical research developing novel immunotherapeutic interventions in the treatment of UPS.
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Affiliation(s)
- Pavla Taborska
- Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Uvalu 84, 150 06 Praha 5, Prague, Czech Republic
| | - Pavol Lukac
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Dmitry Stakheev
- Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Uvalu 84, 150 06 Praha 5, Prague, Czech Republic
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lenka Rajsiglova
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Katerina Kalkusova
- Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Uvalu 84, 150 06 Praha 5, Prague, Czech Republic
| | - Karolina Strnadova
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Faculty of Medicine, BIOCEV, Charles University, Vestec, Czech Republic
| | - Lukas Lacina
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Faculty of Medicine, BIOCEV, Charles University, Vestec, Czech Republic
- Department of Dermatovenerology, First Faculty of Medicine, Charles University, and General University Hospital, Prague, Czech Republic
| | - Barbora Dvorankova
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Faculty of Medicine, BIOCEV, Charles University, Vestec, Czech Republic
| | - Jiri Novotny
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Kolar
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Milena Vrana
- HLA Department, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Cechova
- HLA Department, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Sarka Ransdorfova
- Department of Cytogenetics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Marie Valerianova
- Department of Cytogenetics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Karel Smetana
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- First Faculty of Medicine, BIOCEV, Charles University, Vestec, Czech Republic
| | - Luca Vannucci
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Daniel Smrz
- Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Uvalu 84, 150 06 Praha 5, Prague, Czech Republic.
- Laboratory of Immunotherapy, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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Asins MJ, Bullones A, Raga V, Romero-Aranda MR, Espinosa J, Triviño JC, Bernet GP, Traverso JA, Carbonell EA, Claros MG, Belver A. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus. Int J Mol Sci 2023; 24:15759. [PMID: 37958745 PMCID: PMC10650496 DOI: 10.3390/ijms242115759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The excessive accumulation of chloride (Cl-) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl-, Na+, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (Citrus reshni) and the disease-resistant donor Poncirus trifoliata were performed with the aim to identify repeatable QTLs that regulate leaf Cl- (and/or Na+) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl- was detected in chromosome 6 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided.
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Affiliation(s)
- Maria J. Asins
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Amanda Bullones
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
| | - Veronica Raga
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Maria R. Romero-Aranda
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
| | - Jesus Espinosa
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
| | - Juan C. Triviño
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Guillermo P. Bernet
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Jose A. Traverso
- Department of Cellular Biology, Faculty of Sciences, Universidad de Granada, 18071 Granada, Spain;
| | - Emilio A. Carbonell
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
- CIBER de Enfermedades Raras (CIBERER) U741, 29071 Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Málaga, Spain
| | - Andres Belver
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
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Díaz-Rueda P, Morales de los Ríos L, Romero LC, García I. Old poisons, new signaling molecules: the case of hydrogen cyanide. J Exp Bot 2023; 74:6040-6051. [PMID: 37586035 PMCID: PMC10575699 DOI: 10.1093/jxb/erad317] [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: 04/20/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
The high phenotypic plasticity developed by plants includes rapid responses and adaptations to aggressive or changing environments. To achieve this, they evolved extremely efficient mechanisms of signaling mediated by a wide range of molecules, including small signal molecules. Among them, hydrogen cyanide (HCN) has been largely ignored due to its toxic characteristics. However, not only is it present in living organisms, but it has been shown that it serves several functions in all kingdoms of life. Research using model plants has changed the traditional point of view, and it has been demonstrated that HCN plays a positive role in the plant response to pathogens independently of its toxicity. Indeed, HCN induces a response aimed at protecting the plant from pathogen attack, and the HCN is provided either exogenously (in vitro or by some cyanogenic bacteria species present in the rhizosphere) or endogenously (in reactions involving ethylene, camalexin, or other cyanide-containing compounds). The contribution of different mechanisms to HCN function, including a new post-translational modification of cysteines in proteins, namely S-cyanylation, is discussed here. This work opens up an expanding 'HCN field' of research related to plants and other organisms.
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Affiliation(s)
- Pablo Díaz-Rueda
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092-Sevilla, Spain
| | | | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092-Sevilla, Spain
| | - Irene García
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092-Sevilla, Spain
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28
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Díaz-Rullo J, González-Pastor JE. tRNA queuosine modification is involved in biofilm formation and virulence in bacteria. Nucleic Acids Res 2023; 51:9821-9837. [PMID: 37638766 PMCID: PMC10570037 DOI: 10.1093/nar/gkad667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/27/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
tRNA modifications are crucial for fine-tuning of protein translation. Queuosine (Q) modification of tRNAs is thought to modulate the translation rate of NAU codons, but its physiological role remains elusive. Therefore, we hypothesize that Q-tRNAs control those physiological processes involving NAU codon-enriched genes (Q-genes). Here, we report a novel bioinformatic strategy to predict Q-genes, revealing a widespread enrichment in functions, especially those related to biofilm formation and virulence in bacteria, and particularly in human pathogens. Indeed, we experimentally verified that these processes were significantly affected by altering the degree of tRNA Q-modification in different model bacteria, representing the first report of a general mechanism controlling biofilm formation and virulence in Gram-positive and Gram-negative bacteria possibly through the coordination of the expression of functionally related genes. Furthermore, we propose that changes in Q availability in a microbiome would affect its functionality. Our findings open the door to the control of bacterial infections and biofilm formation by inhibition of tRNA Q-modification.
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Affiliation(s)
- Jorge Díaz-Rullo
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir km 4, Torrejón de Ardoz 28850, Madrid, Spain
| | - José Eduardo González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir km 4, Torrejón de Ardoz 28850, Madrid, Spain
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Chocholouš P, Matoušová K, Šatínský D, Krčmová LK, Sklenářová H. Longevity and other practical benefits of monolithic silica columns in the analysis of samples with complex matrices. J Sep Sci 2023; 46:e2300448. [PMID: 37582639 DOI: 10.1002/jssc.202300448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023]
Abstract
At the turn of the millennium, the monolithic columns invoked new chances in HPLC. Even more than their organic polymer-based siblings, the inorganic silica-based monoliths targeted the territory of classical fully porous particle-packed columns, promising many benefits. Based on the number of published articles, the monoliths attracted academics just in the first few years after their introduction to the market. Lately, as superficially porous particles and sub-2-micron fully porous particles dominated the market, they stayed in the focus of routine laboratories and those who really appreciated the high porosity of the monolithic bed. The monoliths' practical benefits cannot be easily traced in the literature when they gradually lose academics' interest. Nevertheless, after more than 20 years of our experience, we still favor silica monoliths for their low back pressure and longevity when analyzing samples of clinical, pharmaceutical, and environmental origin. At the same time, the high permeability of monoliths enabled the birth of sequential injection chromatography, the medium-pressure separation technique based on the flexible flow manifold. This minireview aims to check, discuss, and summarize the practical aspects of monolithic silica columns in HPLC and medium-pressure sequential injection chromatography (SIC) that may not be visible at first sight but are evident retrospectively.
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Affiliation(s)
- Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Kateřina Matoušová
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Králové, Czech Republic
| | - Dalibor Šatínský
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Lenka Kujovská Krčmová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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Porubiaková O, Havlík J, Indu, Šedý M, Přepechalová V, Bartas M, Bidula S, Šťastný J, Fojta M, Brázda V. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiol Spectr 2023; 11:e0164823. [PMID: 37358458 PMCID: PMC10434271 DOI: 10.1128/spectrum.01648-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023] Open
Abstract
Noncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions. IMPORTANCE Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation.
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Affiliation(s)
- Otília Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Havlík
- Mendel University in Brno, Brno, Czech Republic
| | - Indu
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Šedý
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Veronika Přepechalová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Stefan Bidula
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jiří Šťastný
- Mendel University in Brno, Brno, Czech Republic
- Brno University of Technology, Faculty of Mechanical Engineering, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
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31
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Cortés-Espinar AJ, Ibarz-Blanch N, Soliz-Rueda JR, Bonafos B, Feillet-Coudray C, Casas F, Bravo FI, Calvo E, Ávila-Román J, Mulero M. Rhythm and ROS: Hepatic Chronotherapeutic Features of Grape Seed Proanthocyanidin Extract Treatment in Cafeteria Diet-Fed Rats. Antioxidants (Basel) 2023; 12:1606. [PMID: 37627601 PMCID: PMC10452039 DOI: 10.3390/antiox12081606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Polyphenols play a key role in the modulation of circadian rhythms, while the cafeteria diet (CAF) is able to perturb the hepatic biological rhythm and induce important ROS production. Consequently, we aimed to elucidate whether grape seed proanthocyanidin extract (GSPE) administration recovers the CAF-induced hepatic antioxidant (AOX) misalignment and characterize the chronotherapeutic properties of GSPE. For this purpose, Fischer 344 rats were fed a standard diet (STD) or a CAF and concomitantly treated with GSPE at two time-points (ZT0 vs. ZT12). Animals were euthanized every 6 h and the diurnal rhythms of hepatic ROS-related biomarkers, hepatic metabolites, and AOX gene expression were examined. Interestingly, GSPE treatment was able to recover the diurnal rhythm lost due to the CAF. Moreover, GSPE treatment also increased the acrophase of Sod1, as well as bringing the peak closer to that of the STD group. GSPE also corrected some hepatic metabolites altered by the CAF. Importantly, the differences observed at ZT0 vs. ZT12 due to the time of GSPE administration highlight a chronotherapeutic profile on the proanthocyanin effect. Finally, GSPE could also reduce diet-induced hepatic oxidative stress not only by its ROS-scavenging properties but also by retraining the circadian rhythm of AOX enzymes.
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Affiliation(s)
- Antonio J. Cortés-Espinar
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.J.C.-E.); (N.I.-B.); (J.R.S.-R.); (F.I.B.); (E.C.)
- Nutrigenomics Research Group, Institut d’Investigació Sanitària Pere Virgili, 43007 Tarragona, Spain
- DMEM, EMN, UMR 866, INRAe, Université de Montpellier, 34090 Montpellier, France; (B.B.); (C.F.-C.); (F.C.)
| | - Néstor Ibarz-Blanch
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.J.C.-E.); (N.I.-B.); (J.R.S.-R.); (F.I.B.); (E.C.)
- Nutrigenomics Research Group, Institut d’Investigació Sanitària Pere Virgili, 43007 Tarragona, Spain
| | - Jorge R. Soliz-Rueda
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.J.C.-E.); (N.I.-B.); (J.R.S.-R.); (F.I.B.); (E.C.)
- Nutrigenomics Research Group, Institut d’Investigació Sanitària Pere Virgili, 43007 Tarragona, Spain
| | - Béatrice Bonafos
- DMEM, EMN, UMR 866, INRAe, Université de Montpellier, 34090 Montpellier, France; (B.B.); (C.F.-C.); (F.C.)
| | - Christine Feillet-Coudray
- DMEM, EMN, UMR 866, INRAe, Université de Montpellier, 34090 Montpellier, France; (B.B.); (C.F.-C.); (F.C.)
| | - François Casas
- DMEM, EMN, UMR 866, INRAe, Université de Montpellier, 34090 Montpellier, France; (B.B.); (C.F.-C.); (F.C.)
| | - Francisca Isabel Bravo
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.J.C.-E.); (N.I.-B.); (J.R.S.-R.); (F.I.B.); (E.C.)
- Nutrigenomics Research Group, Institut d’Investigació Sanitària Pere Virgili, 43007 Tarragona, Spain
| | - Enrique Calvo
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.J.C.-E.); (N.I.-B.); (J.R.S.-R.); (F.I.B.); (E.C.)
- Nutrigenomics Research Group, Institut d’Investigació Sanitària Pere Virgili, 43007 Tarragona, Spain
| | - Javier Ávila-Román
- Molecular and Applied Pharmacology Group (FARMOLAP), Department of Pharmacology, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Miquel Mulero
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.J.C.-E.); (N.I.-B.); (J.R.S.-R.); (F.I.B.); (E.C.)
- Nutrigenomics Research Group, Institut d’Investigació Sanitària Pere Virgili, 43007 Tarragona, Spain
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Brázda V, Dobrovolná M, Bohálová N, Mergny JL. G-quadruplexes in the evolution of hepatitis B virus. Nucleic Acids Res 2023; 51:7198-7204. [PMID: 37395407 PMCID: PMC10415126 DOI: 10.1093/nar/gkad556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/23/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of 'genetic camouflage' to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
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Petrzik K. Peptidoglycan Endopeptidase from Novel Adaiavirus Bacteriophage Lyses Pseudomonas aeruginosa Strains as Well as Arthrobacter globiformis and A. pascens Bacteria. Microorganisms 2023; 11:1888. [PMID: 37630448 PMCID: PMC10458142 DOI: 10.3390/microorganisms11081888] [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: 07/04/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
A novel virus lytic for Pseudomonas aeruginosa has been purified. Its viral particles have a siphoviral morphology with a head 60 nm in diameter and a noncontractile tail 184 nm long. The dsDNA genome consists of 16,449 bp, has cohesive 3' termini, and encodes 28 putative proteins in a single strain. The peptidoglycan endopeptidase encoded by ORF 16 was found to be the lytic enzyme of this virus. The recombinant, purified enzyme was active up to 55 °C in the pH range 6-9 against all tested isolates of P. aeruginosa, but, surprisingly, also against the distant Gram-positive micrococci Arthrobacter globiformis and A. pascens. Both this virus and its endolysin are further candidates for possible treatment against P. aeruginosa and probably also other bacteria.
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Affiliation(s)
- Karel Petrzik
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branisovska 1160/31, 370 05 Ceske Budejovice, Czech Republic
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34
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Ruiz-García A, Al-Obaidi MA, Nuez I, Mujtaba IM. Impact of SWMM Fouling and Position on the Performance of SWRO Systems in Operating Conditions of Minimum SEC. Membranes (Basel) 2023; 13:676. [PMID: 37505042 PMCID: PMC10385730 DOI: 10.3390/membranes13070676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/02/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023]
Abstract
Due to water stress in the world in general desalination technologies are becoming increasingly important. Among the available technologies, reverse osmosis (RO) is the most widespread due to its reliability and efficiency compared to other technologies. The main weakness of RO is the loss of performance due to membrane fouling, which usually affects the water permeability coefficient (A), causing it to decrease. In RO desalination plants, fouling does not affect all spiral wound membrane modules (SWMMs) in the pressure vessels (PVs) in the same way. This will depend on the type of fouling and the position of the SWMM inside the PV. In this study, the impact of A and the position of the SWMM on the performance of the RO system is analyzed. For this purpose, decrements of up to 50% have been assumed for the seven SWMMs in series considering nine commercial SWMM models. The operating point analyzed is that which minimizes the specific energy consumption (SEC), a point obtained in a previous work carried out by the authors. The results show how the impact of A on the SWMM in the first position is more significant than the impact on modules that are in another position for the nine SWRO models studied. A drop of 50% in the coefficient A of the first element produces a permeate loss in the pressure pipe between 0.67 and 1.35 m3 d-1. Furthermore, it was observed that the models with the lowest coefficient A exhibited the highest performance losses in terms of permeate production when A was decreased.
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Affiliation(s)
- Alejandro Ruiz-García
- Department of Electronic Engineering and Automation, University of Las Palmas de Gran Canaria, Campus Universitario de Tafira, 35017 Las Palmas de Gran Canaria, Spain
| | - Mudhar A Al-Obaidi
- Department of Computer Techniques, Technical Institute of Baquba, Middle Technical University, Baquba 00964, Iraq
| | - Ignacio Nuez
- Department of Electronic Engineering and Automation, University of Las Palmas de Gran Canaria, Campus Universitario de Tafira, 35017 Las Palmas de Gran Canaria, Spain
| | - Iqbal M Mujtaba
- Department of Chemical Engineering, Faculty of Engineering and Informatics, University of Bradford, Bradford BD7 1DP, UK
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Milenkovic I, Santos Vieira HG, Lucas MC, Ruiz-Orera J, Patone G, Kesteven S, Wu J, Feneley M, Espadas G, Sabidó E, Hübner N, van Heesch S, Völkers M, Novoa EM. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res 2023; 51:5301-5324. [PMID: 36882085 PMCID: PMC10287911 DOI: 10.1093/nar/gkad121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. We identify a rescue mechanism in which, upon RPL3L depletion, RPL3 becomes up-regulated, yielding RPL3-containing ribosomes instead of RPL3L-containing ribosomes that are typically found in cardiomyocytes. Using both ribosome profiling (Ribo-seq) and a novel orthogonal approach consisting of ribosome pulldown coupled to nanopore sequencing (Nano-TRAP), we find that RPL3L modulates neither translational efficiency nor ribosome affinity towards a specific subset of transcripts. In contrast, we show that depletion of RPL3L leads to increased ribosome-mitochondria interactions in cardiomyocytes, which is accompanied by a significant increase in ATP levels, potentially as a result of fine-tuning of mitochondrial activity. Our results demonstrate that the existence of tissue-specific RP paralogues does not necessarily lead to enhanced translation of specific transcripts or modulation of translational output. Instead, we reveal a complex cellular scenario in which RPL3L modulates the expression of RPL3, which in turn affects ribosomal subcellular localization and, ultimately, mitochondrial activity.
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Affiliation(s)
- Ivan Milenkovic
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Morghan C Lucas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Scott Kesteven
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Jianxin Wu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Michael Feneley
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
- Charité -Universitätsmedizin, D-10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, D-13347 Berlin, Germany
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Gomis-Font MA, Sastre-Femenia MÀ, Taltavull B, Cabot G, Oliver A. In vitro dynamics and mechanisms of cefiderocol resistance development in wild-type, mutator and XDR Pseudomonas aeruginosa. J Antimicrob Chemother 2023:7186575. [PMID: 37253034 DOI: 10.1093/jac/dkad172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/14/2023] [Indexed: 06/01/2023] Open
Abstract
OBJECTIVES To analyse the dynamics and mechanisms of stepwise resistance development to cefiderocol in Pseudomonas aeruginosa. METHODS Cefiderocol resistance evolution was analysed in WT PAO1, PAOMS (mutS mutator derivate) and three XDR clinical isolates belonging to ST111, ST175 and ST235 clones. Strains were incubated in triplicate experiments for 24 h in iron-depleted CAMHB with 0.06-128 mg/L cefiderocol. Tubes from the highest antibiotic concentration showing growth were reinoculated into fresh medium containing concentrations up to 128 mg/L for 7 consecutive days. Two colonies per strain and experiment were characterized by determining the susceptibility profiles and WGS. RESULTS Evolution of resistance was significantly enhanced in PAOMS, but was variable for the XDR strains, including levels similar to PAOMS (ST235), similar to PAO1 (ST175) or even below PAO1 (ST111). WGS revealed 2-5 mutations for PAO1 lineages and 35-58 for PAOMS. The number of mutations in the XDR clinical strains ranged from 2 to 4 except for one of the ST235 experiments in which a mutL lineage was selected, thus increasing the number of mutations. The most frequently mutated genes were piuC, fptA and pirR, related to iron uptake. Additionally, an L320P AmpC mutation was selected in multiple lineages and cloning confirmed its major impact on cefiderocol (but not ceftolozane/tazobactam or ceftazidime/avibactam) resistance. Mutations in CpxS and PBP3 were also documented. CONCLUSIONS This work deciphers the potential resistance mechanisms that may emerge upon the introduction of cefiderocol into clinical practice, and highlights that the risk of resistance development might be strain-specific even for XDR high-risk clones.
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Affiliation(s)
- María A Gomis-Font
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, Spain
| | - Miquel À Sastre-Femenia
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, Spain
| | - Biel Taltavull
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, Spain
| | - Gabriel Cabot
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, Spain
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Kapitanov IV, Sudheer SM, Yadav T, Ghosh KK, Gathergood N, Gupta VK, Karpichev Y. Sustainable Phenylalanine-Derived SAILs for Solubilization of Polycyclic Aromatic Hydrocarbons. Molecules 2023; 28:molecules28104185. [PMID: 37241924 DOI: 10.3390/molecules28104185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
The solubilization capacity of a series of sustainable phenylalanine-derived surface-active ionic liquids (SAILs) was evaluated towards polycyclic aromatic hydrocarbons-naphthalene, anthracene and pyrene. The key physico-chemical parameters of the studied systems (critical micelle concentration, spectral properties, solubilization parameters) were determined, analyzed and compared with conventional cationic surfactant, CTABr. For all studied PAH solubilization capacity increases with extension of alkyl chain length of PyPheOCn SAILs reaching the values comparable to CTABr for SAILs with n = 10-12. A remarkable advantage of the phenylalanine-derived SAILs PyPheOCn and PyPheNHCn is a possibility to cleave enzymatically ester and/or amide bonds under mild conditions, to separate polycyclic aromatic hydrocarbons in situ. A series of immobilized enzymes was tested to determine the most suitable candidates for tunable decomposition of SAILs. The decomposition pathway could be adjusted depending on the choice of the enzyme system, reaction conditions, and selection of SAILs type. The evaluated systems can provide selective cleavage of the ester and amide bond and help to choose the optimal decomposition method of SAILs for enzymatic recycling of SAILs transformation products or as a pretreatment towards biological mineralization. The concept of a possible practical application of studied systems for PAHs solubilization/separation was also discussed focusing on sustainability and a green chemistry approach.
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Affiliation(s)
- Illia V Kapitanov
- Department of Chemistry and Biotechnology, Tallinn University of Technology (TalTech), 12618 Tallinn, Estonia
| | - Surya M Sudheer
- Department of Chemistry and Biotechnology, Tallinn University of Technology (TalTech), 12618 Tallinn, Estonia
| | - Toshikee Yadav
- Department of Chemistry and Biotechnology, Tallinn University of Technology (TalTech), 12618 Tallinn, Estonia
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 92010, India
| | - Kallol K Ghosh
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 92010, India
| | - Nicholas Gathergood
- School of Chemistry, College of Science, University of Lincoln, Lincoln LN6 7TS, UK
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, Tallinn University of Technology (TalTech), 12618 Tallinn, Estonia
- Biorefining and Advanced Materials Research Centre, SRUC, Parkgate, Dumfries DG1 3NE, UK
| | - Yevgen Karpichev
- Department of Chemistry and Biotechnology, Tallinn University of Technology (TalTech), 12618 Tallinn, Estonia
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Merlo A, Duminica F, Daniel A, Léonard G. Techno-Economic Analysis and Life Cycle Assessment of High-Velocity Oxy-Fuel Technology Compared to Chromium Electrodeposition. Materials (Basel) 2023; 16:ma16103678. [PMID: 37241305 DOI: 10.3390/ma16103678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023]
Abstract
Due to the toxicity associated with chromium electrodeposition, alternatives to that process are highly sought after. One of those potential alternatives is High Velocity Oxy-Fuel (HVOF). In this work, a HVOF installation is compared with chromium electrodeposition from environmental and economic points of view by using Life Cycle Assessment (LCA) and Techno-Economic Analysis (TEA) for the evaluation. Costs and environmental impacts per piece coated are then evaluated. On an economic side, the lower labor requirements of HVOF allow one to noticeably reduce the costs (20.9% reduction) per functional unit (F.U.). Furthermore, on an environmental side, HVOF has a lower impact for the toxicity compared to electrodeposition, even if the results are a bit more mixed in other impact categories.
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Affiliation(s)
- Antoine Merlo
- Department of Chemical Engineering, University of Liège, Quartier Agora B6a Sart-Tilman, 4000 Liège, Belgium
| | - Florin Duminica
- Centre de Recherches Métallurgiques, CRMGroup, Avenue du Bois Saint-Jean, 21, 4000 Liège, Belgium
| | - Alain Daniel
- Centre de Recherches Métallurgiques, CRMGroup, Avenue du Bois Saint-Jean, 21, 4000 Liège, Belgium
| | - Grégoire Léonard
- Department of Chemical Engineering, University of Liège, Quartier Agora B6a Sart-Tilman, 4000 Liège, Belgium
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Trujillo C, Pérez-Arantegui J, Lobinski R, Laborda F. Improving the Detectability of Microplastics in River Waters by Single Particle Inductively Coupled Plasma Mass Spectrometry. Nanomaterials (Basel) 2023; 13:nano13101582. [PMID: 37241999 DOI: 10.3390/nano13101582] [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] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
Detection of microplastics in environmental samples requires fast, sensitive and selective analytical techniques, both in terms of the size of the microparticles and their concentration. Single particle inductively coupled plasma mass spectrometry (SP-ICP-MS) allows the detection of plastic particles down to ca. 1 µm and down to concentrations of 100 particles per mL. In SP-ICP-MS, detection of carbon-containing particles is hampered by the presence of other forms of carbon (carbonates, organic matter, microorganisms…). An acidic pre-treatment of river water samples with 10% (v/v) nitric acid for 24 h allowed the reduction of the presence of dissolved carbon to ultrapure water levels and the digestion of potential microorganisms in the samples, recovering polystyrene microparticles up to 80%. Carbon-containing particles were detected in most of the samples analysed from Spanish and French Pyrenean rivers. The presence of microplastics in these samples was confirmed by Raman microscopy and their morphology was defined by electron microscopy combined with energy-dispersive X-ray spectroscopy. The developed SP-ICP-MS method is suitable for the rapid screening of river waters for the presence of microplastics, which can then be analysed by inherently slower but more selective techniques (e.g., Raman microscopy).
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Affiliation(s)
- Celia Trujillo
- Group of Analytical Spectroscopy and Sensors (GEAS), Institute of Environmental Sciences (IUCA), University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Josefina Pérez-Arantegui
- Group of Analytical Spectroscopy and Sensors (GEAS), Institute of Environmental Sciences (IUCA), University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Ryszard Lobinski
- IPREM UMR 5254, CNRS, E2S UPPA, Université de Pau et des Pays de L'Adour, Hélioparc, 64053 Pau, France
- Chair of Analytical Chemistry, Department of Chemistry, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warszawa, Poland
| | - Francisco Laborda
- Group of Analytical Spectroscopy and Sensors (GEAS), Institute of Environmental Sciences (IUCA), University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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Mao W, Fu X, Wu Z, Zhang J, Ling Z, Liu Y, Zhao YYS, Changela HG, Ni Y, Yan F, Zou Y. Solid-gas carbonate formation during dust events on Mars. Natl Sci Rev 2023; 10:nwac293. [PMID: 36960225 PMCID: PMC10029838 DOI: 10.1093/nsr/nwac293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Electrostatic discharge experiments under simulated martian atmospheric conditions indicate that atmospheric CO2 has been sequestered into carbonate by the Mars dust activities during the Amazonia era.
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Affiliation(s)
- Wenshuo Mao
- Shandong Key Laboratory of Optical Astronomy and Solar-Terrestrial Environment, School of Space Science and Physics, Institute of Space Sciences, Shandong University, China
| | | | | | - Jiang Zhang
- Shandong Key Laboratory of Optical Astronomy and Solar-Terrestrial Environment, School of Space Science and Physics, Institute of Space Sciences, Shandong University, China
| | - Zongcheng Ling
- Shandong Key Laboratory of Optical Astronomy and Solar-Terrestrial Environment, School of Space Science and Physics, Institute of Space Sciences, Shandong University, China
- CAS Center for Excellence in Comparative Planetology, China
| | - Yang Liu
- State Key Laboratory of Space Weather, National Space Science Center, Chinese Academy of Sciences, China
| | - Yu-Yan Sara Zhao
- International Center for Planetary Science, College of Earth Science, Chengdu University of Technology, China
- CAS Center for Excellence in Comparative Planetology, China
| | - Hitesh G Changela
- J’Heyrovski Institute of Physical Chemistry, Czech Academy of Sciences, Czech Republic
- Department of Earth & Planetary Science, University of New Mexico, USA
| | - Yuheng Ni
- Shandong Key Laboratory of Optical Astronomy and Solar-Terrestrial Environment, School of Space Science and Physics, Institute of Space Sciences, Shandong University, China
| | - Fabao Yan
- School of Mechanical, Electrical & Information Engineering, Shandong University, China
| | - Yongliao Zou
- State Key Laboratory of Space Weather, National Space Science Center, Chinese Academy of Sciences, China
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Jimeno R, Mouron S, Salgado R, Loi S, Pérez-Mies B, Sánchez-Bayona R, Manso L, Martínez M, Garrido-García A, Serrano-Pardo R, Colomer R, Quintela-Fandino M. Tumor P70S6K hyperactivation is inversely associated with tumor-infiltrating lymphocytes in triple-negative breast cancer. Clin Transl Oncol 2023; 25:1124-1131. [PMID: 36508123 PMCID: PMC10025236 DOI: 10.1007/s12094-022-03006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/07/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is characterized by large heterogeneity and relative lack of available targeted therapies. To find therapeutic strategies for distinct patients with TNBC, several approaches have been used for TNBC clustering, including recently immune and phosphoproteomic patterns. Based on 70-kDa ribosomal protein S6 kinase (P70S6K)-TNBC clustering, the current study explores the immune profiling in TNBC tumors. METHODS Stromal tumor-infiltrating lymphocytes (sTILs) were evaluated in human TNBC tumor samples. Furthermore, immunohistochemistry staining for CD8, CD4, Foxp3, and CD20 was performed in tissue microarrays (TMA) sections. RESULTS Histological analysis showed decreased sTILs, CD20+ cells, and CD8+/CD4+ ratio in high phosphorylated P70S6K (p-P70S6K) tumors. Moreover, p-P70S6K score was directly correlated with CD4+ and Foxp3+ T cells, while it was inversely correlated with CD8+/CD4+ and CD8+/Foxp3+ ratios. CONCLUSION sTIL infiltration and lymphocyte profiling vary in the context of hyperactivation of P70S6K in TNBC tumors.
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Affiliation(s)
- Rebeca Jimeno
- Breast Cancer Clinical Research Unit, Clinical Research Program, CNIO, Madrid, Spain
| | - Silvana Mouron
- Breast Cancer Clinical Research Unit, Clinical Research Program, CNIO, Madrid, Spain
| | - Roberto Salgado
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, GZA-ZNA, Antwerp, Belgium
| | - Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Cancer Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Belén Pérez-Mies
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRyCIS), Madrid, Spain
- Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Spain
- CIBERONC, Madrid, Spain
| | | | - Luis Manso
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Mario Martínez
- Department of Pathology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Ana Garrido-García
- Department of Medical Oncology, Hospital Universitario La Princesa, Madrid, Spain
| | | | - Ramón Colomer
- Department of Medical Oncology, Hospital Universitario La Princesa, Madrid, Spain
- Department of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Quintela-Fandino
- Breast Cancer Clinical Research Unit, Clinical Research Program, CNIO, Madrid, Spain.
- Medical Oncology, Hospital Universitario de Fuenlabrada, Madrid, Spain.
- Endowed Chair of Personalised Precision Medicine, Department of Medicine, Universidad Autónoma de Madrid, Madrid, Spain.
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Sánchez-Gaya V, Rada-Iglesias A. POSTRE: a tool to predict the pathological effects of human structural variants. Nucleic Acids Res 2023; 51:e54. [PMID: 36999617 DOI: 10.1093/nar/gkad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Understanding the pathological impact of non-coding genetic variation is a major challenge in medical genetics. Accumulating evidences indicate that a significant fraction of genetic alterations, including structural variants (SVs), can cause human disease by altering the function of non-coding regulatory elements, such as enhancers. In the case of SVs, described pathomechanisms include changes in enhancer dosage and long-range enhancer-gene communication. However, there is still a clear gap between the need to predict and interpret the medical impact of non-coding variants, and the existence of tools to properly perform these tasks. To reduce this gap, we have developed POSTRE (Prediction Of STRuctural variant Effects), a computational tool to predict the pathogenicity of SVs implicated in a broad range of human congenital disorders. By considering disease-relevant cellular contexts, POSTRE identifies SVs with either coding or long-range pathological consequences with high specificity and sensitivity. Furthermore, POSTRE not only identifies pathogenic SVs, but also predicts the disease-causative genes and the underlying pathological mechanism (e.g, gene deletion, enhancer disconnection, enhancer adoption, etc.). POSTRE is available at https://github.com/vicsanga/Postre.
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Affiliation(s)
- Víctor Sánchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain
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Šemberová K, Svitok M, Marhold K, Suda J, Schmickl RE. Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes. Ann Bot 2023; 131:71-86. [PMID: 34559179 PMCID: PMC9904352 DOI: 10.1093/aob/mcab123] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, the possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids (e.g. tetraploids and hexaploids). Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of ploidy level and the environment to morphology have generally been neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones. METHODS Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology. KEY RESULTS Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype. CONCLUSIONS Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype highlights the role of polyploidy in reproductive isolation.
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Affiliation(s)
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, T. G. Masaryka, Zvolen, Slovakia
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Karol Marhold
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta, Bratislava, Slovakia
| | | | - Roswitha E Schmickl
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Department of Evolutionary Plant Biology, Zámek, Průhonice, Czech Republic
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Pacheco PJ, Cabrera JJ, Jiménez-Leiva A, Torres MJ, Gates AJ, Bedmar EJ, Richardson DJ, Mesa S, Tortosa G, Delgado MJ. The copper-responsive regulator CsoR is indirectly involved in Bradyrhizobium diazoefficiens denitrification. FEMS Microbiol Lett 2023; 370:fnad084. [PMID: 37573143 PMCID: PMC10457146 DOI: 10.1093/femsle/fnad084] [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: 05/16/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
The soybean endosymbiont Bradyrhizobium diazoefficiens harbours the complete denitrification pathway that is catalysed by a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a nitrous oxide reductase (Nos), encoded by the napEDABC, nirK, norCBQD, and nosRZDFYLX genes, respectively. Induction of denitrification genes requires low oxygen and nitric oxide, both signals integrated into a complex regulatory network comprised by two interconnected cascades, FixLJ-FixK2-NnrR and RegSR-NifA. Copper is a cofactor of NirK and Nos, but it has also a role in denitrification gene expression and protein synthesis. In fact, Cu limitation triggers a substantial down-regulation of nirK, norCBQD, and nosRZDFYLX gene expression under denitrifying conditions. Bradyrhizobium diazoefficiens genome possesses a gene predicted to encode a Cu-responsive repressor of the CsoR family, which is located adjacent to copA, a gene encoding a putative Cu+-ATPase transporter. To investigate the role of CsoR in the control of denitrification gene expression in response to Cu, a csoR deletion mutant was constructed in this work. Mutation of csoR did not affect the capacity of B. diazoefficiens to grow under denitrifying conditions. However, by using qRT-PCR analyses, we showed that nirK and norCBQD expression was much lower in the csoR mutant compared to wild-type levels under Cu-limiting denitrifying conditions. On the contrary, copA expression was significantly increased in the csoR mutant. The results obtained suggest that CsoR acts as a repressor of copA. Under Cu limitation, CsoR has also an indirect role in the expression of nirK and norCBQD genes.
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Affiliation(s)
- Pedro J Pacheco
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Juan J Cabrera
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Andrea Jiménez-Leiva
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - María J Torres
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
- Department of Biochemistry and Molecular Biology, Campus Universitario de Rabanales, University of Córdoba, Ed. C6, Planta Baja, 14071 Córdoba, Spain
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
| | - Eulogio J Bedmar
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
| | - Socorro Mesa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Germán Tortosa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - María J Delgado
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
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De Diego N, Spíchal L. Presence and future of plant phenotyping approaches in biostimulant research and development. J Exp Bot 2022; 73:5199-5212. [PMID: 35770872 PMCID: PMC9440437 DOI: 10.1093/jxb/erac275] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/20/2022] [Indexed: 06/01/2023]
Abstract
Commercial interest in biostimulants as a tool for sustainable green economics and agriculture concepts is on a steep rise, being followed by increasing demand to employ efficient scientific methods to develop new products and understand their mechanisms of action. Biostimulants represent a highly diverse group of agents derived from various natural sources. Regardless of their nutrition content and composition, they are classified by their ability to improve crop performance through enhanced nutrient use efficiency, abiotic stress tolerance, and quality of crops. Numerous reports have described modern, non-invasive sensor-based phenotyping methods in plant research. This review focuses on applying phenotyping approaches in biostimulant research and development, and maps the evolution of interaction of these two intensively growing domains. How phenotyping served to identify new biostimulants, the description of their biological activity, and the mechanism/mode of action are summarized. Special attention is dedicated to the indoor high-throughput methods using model plants suitable for biostimulant screening and developmental pipelines, and high-precision approaches used to determine biostimulant activity. The need for a complex method of testing biostimulants as multicomponent products through integrating other -omic approaches followed by advanced statistical/mathematical tools is emphasized.
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Affiliation(s)
- Nuria De Diego
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů, Olomouc, Czech Republic
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Sainnokhoi TA, Kováts N, Gelencsér A, Hubai K, Teke G, Pelden B, Tserenchimed T, Erdenechimeg Z, Galsuren J. Characteristics of particle-bound polycyclic aromatic hydrocarbons (PAHs) in indoor PM 2.5 of households in the Southwest part of Ulaanbaatar capital, Mongolia. Environ Monit Assess 2022; 194:665. [PMID: 35951250 PMCID: PMC9372015 DOI: 10.1007/s10661-022-10297-0] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Air pollution, including PM2.5 concentration in Ulaanbaatar (capital of Mongolia) is a serious matter of concern. As the majority of households use coal in large areas of the city, indoor air quality is also posing a serious risk to human health. This study investigated the concentration of polycyclic aromatic compounds (PAHs) in indoor particulate matter (PM2.5) in 10 non-smoker households. Sampling was conducted in winter of 2018, between 27 January and 09 February. Concentrations of PM2.5 in the indoor air of households ranged between 62.8 and 324.8 µg m-3. Total concentration of PAHs also varied in a relatively wide range, between 46.2 and 175.7 ng m-3. Five-ring PAHs represented a considerably high fraction of total PAHs between 25 and 53%, benzo[b]fluoranthene (BbF) and benzo[a]pyrene (BaP) were the two predominant compounds within five-ring PAHs. Significant correlation was found between indoor and outdoor particulate matter levels in wintertime. Considering individual characteristic PAHs, heavier PAHs homologues (4- to 5-ring and 6-ring PAHs) were detected in all households, which suggested the influence of coal combustion and traffic exhaust. Health risk of children attributed to PAHs inhalation was assessed by taking into account the lifetime-average daily dose (LADD) and corresponding lifetime cancer risk. Lifetime average daily dose for children in only one household were slightly higher than health-based guideline level (1.0 × 10-5), defined by WHO, whereas LADD for adults and children of other households were within acceptable limit. The cancer risks from the exposure of children to air pollutants in all households except HH-3 were found high. In the Vibrio fischeri bioluminescence inhibition assay, according to the toxic unit (TU) values of indoor PM2.5 from ten households, all samples were classified as toxic.
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Affiliation(s)
- Tsend-Ayush Sainnokhoi
- Centre for Natural Sciences, University of Pannonia, Egyetem street 10, Veszprém, 8200, Hungary.
- School of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul District, 17042, Ulaanbaatar, Mongolia.
| | - Nora Kováts
- Centre for Natural Sciences, University of Pannonia, Egyetem street 10, Veszprém, 8200, Hungary
| | - András Gelencsér
- Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Egyetem str. 10, Veszprém, 8200, Hungary
| | - Katalin Hubai
- Centre for Natural Sciences, University of Pannonia, Egyetem street 10, Veszprém, 8200, Hungary
| | - Gábor Teke
- ELGOSCAR-2000 Environmental Technology and Water Management Ltd, 8184, Balatonfűzfő, Hungary
| | - Bolormaa Pelden
- School of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul District, 17042, Ulaanbaatar, Mongolia
| | - Tsagaan Tserenchimed
- School of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul District, 17042, Ulaanbaatar, Mongolia
| | - Zoljargal Erdenechimeg
- School of Public Health, Mongolian National University of Medical Sciences, Zorig street, Ulaanbaatar, 14210, Mongolia
| | - Jargalsaikhan Galsuren
- School of Public Health, Mongolian National University of Medical Sciences, Zorig street, Ulaanbaatar, 14210, Mongolia
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Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
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Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
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Morana O, Nieto‐Garai JA, Björkholm P, Bernardino de la Serna J, Terrones O, Arboleya A, Ciceri D, Rojo‐Bartolomé I, Blouin CM, Lamaze C, Lorizate M, Contreras F. Identification of a New Cholesterol-Binding Site within the IFN-γ Receptor that is Required for Signal Transduction. Adv Sci (Weinh) 2022; 9:e2105170. [PMID: 35166455 PMCID: PMC9008429 DOI: 10.1002/advs.202105170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/26/2022] [Indexed: 05/05/2023]
Abstract
The cytokine interferon-gamma (IFN-γ) is a master regulator of innate and adaptive immunity involved in a broad array of human diseases that range from atherosclerosis to cancer. IFN-γ exerts it signaling action by binding to a specific cell surface receptor, the IFN-γ receptor (IFN-γR), whose activation critically depends on its partition into lipid nanodomains. However, little is known about the impact of specific lipids on IFN-γR signal transduction activity. Here, a new conserved cholesterol (chol) binding motif localized within its single transmembrane domain is identified. Through direct binding, chol drives the partition of IFN-γR2 chains into plasma membrane lipid nanodomains, orchestrating IFN-γR oligomerization and transmembrane signaling. Bioinformatics studies show that the signature sequence stands for a conserved chol-binding motif presented in many mammalian membrane proteins. The discovery of chol as the molecular switch governing IFN-γR transmembrane signaling represents a significant advance for understanding the mechanism of lipid selectivity by membrane proteins, but also for figuring out the role of lipids in modulating cell surface receptor function. Finally, this study suggests that inhibition of the chol-IFNγR2 interaction may represent a potential therapeutic strategy for various IFN-γ-dependent diseases.
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Affiliation(s)
- Ornella Morana
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Jon Ander Nieto‐Garai
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Patrik Björkholm
- Center for Biomembrane ResearchDepartment of Biochemistry and BiophysicsStockholm UniversityStockholmSE‐106 91Sweden
- Science for Life LaboratoryStockholm UniversitySolnaSE‐171 21Sweden
| | - Jorge Bernardino de la Serna
- National Heart and Lung InstituteFaculty of MedicineImperial College LondonSouth KensingtonSir Alexander Fleming BuildingLondonSW7 2AZUK
- Central Laser FacilityRutherford Appleton LaboratoryMRC‐Research Complex at HarwellScience and Technology Facilities CouncilHarwellOX11 0QXUK
- NIHR Imperial Biomedical Research CentreLondonSW7 2AZUK
| | - Oihana Terrones
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Aroa Arboleya
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Dalila Ciceri
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Iratxe Rojo‐Bartolomé
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Cédric M. Blouin
- Institut Curie ‐ Centre de RecherchePSL Research UniversityMembrane Mechanics and Dynamics of Intracellular Signaling LaboratoryParis75248France
- Institut National de la Santé et de la Recherche Médicale (INSERM)ParisU1143France
- Centre National de la Recherche Scientifique (CNRS)UMR 3666Paris75248France
| | - Christophe Lamaze
- Institut Curie ‐ Centre de RecherchePSL Research UniversityMembrane Mechanics and Dynamics of Intracellular Signaling LaboratoryParis75248France
- Institut National de la Santé et de la Recherche Médicale (INSERM)ParisU1143France
- Centre National de la Recherche Scientifique (CNRS)UMR 3666Paris75248France
| | - Maier Lorizate
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Francesc‐Xabier Contreras
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- IKERBASQUEBasque Foundation for ScienceBilbao48011Spain
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Colomer-Vilaplana A, Murga-Moreno J, Canalda-Baltrons A, Inserte C, Soto D, Coronado-Zamora M, Barbadilla A, Casillas S. PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans. Nucleic Acids Res 2022; 50:D1069-D1076. [PMID: 34664660 PMCID: PMC8728255 DOI: 10.1093/nar/gkab925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022] Open
Abstract
Adaptive challenges that humans faced as they expanded across the globe left specific molecular footprints that can be decoded in our today's genomes. Different sets of metrics are used to identify genomic regions that have undergone selection. However, there are fewer methods capable of pinpointing the allele ultimately responsible for this selection. Here, we present PopHumanVar, an interactive online application that is designed to facilitate the exploration and thorough analysis of candidate genomic regions by integrating both functional and population genomics data currently available. PopHumanVar generates useful summary reports of prioritized variants that are putatively causal of recent selective sweeps. It compiles data and graphically represents different layers of information, including natural selection statistics, as well as functional annotations and genealogical estimations of variant age, for biallelic single nucleotide variants (SNVs) of the 1000 Genomes Project phase 3. Specifically, PopHumanVar amasses SNV-based information from GEVA, SnpEFF, GWAS Catalog, ClinVar, RegulomeDB and DisGeNET databases, as well as accurate estimations of iHS, nSL and iSAFE statistics. Notably, PopHumanVar can successfully identify known causal variants of frequently reported candidate selection regions, including EDAR in East-Asians, ACKR1 (DARC) in Africans and LCT/MCM6 in Europeans. PopHumanVar is open and freely available at https://pophumanvar.uab.cat.
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Affiliation(s)
- Aina Colomer-Vilaplana
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jesús Murga-Moreno
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Aleix Canalda-Baltrons
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Clara Inserte
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Daniel Soto
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Marta Coronado-Zamora
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
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50
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Gutierrez‐Fernandez E, Scaccabarozzi AD, Basu A, Solano E, Anthopoulos TD, Martín J. Y6 Organic Thin-Film Transistors with Electron Mobilities of 2.4 cm 2 V -1 s -1 via Microstructural Tuning. Adv Sci (Weinh) 2022; 9:e2104977. [PMID: 34854574 PMCID: PMC8728851 DOI: 10.1002/advs.202104977] [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: 11/03/2021] [Indexed: 06/13/2023]
Abstract
There is a growing demand to attain organic materials with high electron mobility, μe , as current reliable reported values are significantly lower than those exhibited by their hole mobility counterparts. Here, it is shown that a well-known nonfullerene-acceptor commonly used in organic solar cells, that is, BTP-4F (aka Y6), enables solution-processed organic thin-film transistors (OTFT) with a μe as high as 2.4 cm2 V-1 s-1 . This value is comparable to those of state-of-the-art n-type OTFTs, opening up a plethora of new possibilities for this class of materials in the field of organic electronics. Such efficient charge transport is linked to a readily achievable highly ordered crystalline phase, whose peculiar structural properties are thoroughly discussed. This work proves that structurally ordered nonfullerene acceptors can exhibit intrinsically high mobility and introduces a new approach in the quest of high μe organic materials, as well as new guidelines for future materials design.
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Affiliation(s)
| | - Alberto D. Scaccabarozzi
- King Abdullah University of Science and Technology (KAUST)KAUST Solar Center (KSC)Thuwal23955Saudi Arabia
| | - Aniruddha Basu
- King Abdullah University of Science and Technology (KAUST)KAUST Solar Center (KSC)Thuwal23955Saudi Arabia
| | - Eduardo Solano
- ALBA Synchrotron Light SourceNCD‐SWEET BeamlineCerdanyola del Vallès08290Spain
| | - Thomas D. Anthopoulos
- King Abdullah University of Science and Technology (KAUST)KAUST Solar Center (KSC)Thuwal23955Saudi Arabia
| | - Jaime Martín
- POLYMATUniversity of the Basque CountryUPV/EHUAv. de Tolosa 72San Sebastián20018Spain
- Ikerbasque Basque Foundation for ScienceBilbao48013Spain
- University of A CoruñaGroup of PolymersCentro de Investigacións Tecnolóxicas (CIT)Esteiro CampusFerrol15471Spain
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