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Kwiatkowski G, Czyzynska-Cichon I, Tielemans B, Geerkens L, Jasztal A, Velde GV, Chłopicki S. Retrospectively gated ultrashort-echo-time MRI T 1 mapping reveals compromised pulmonary microvascular NO-dependent function in a murine model of acute lung injury. NMR Biomed 2024; 37:e5105. [PMID: 38225796 DOI: 10.1002/nbm.5105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024]
Abstract
This study sought to develop noninvasive, in vivo imaging schemes that allow for quantitative assessment of pulmonary microvascular functional status based on the combination of pulmonary T1 mapping and dynamic contrast-enhanced (DynCE) imaging. Ultrashort-echo-time (UTE) imaging at 9.4 T of lung parenchyma was performed. Retrospective gating was based on modulation of the first point in each recorded spoke. T1 maps were obtained using a series of five consecutive images with varying RF angles and analyzed with the variable flip angle approach. The obtained mean T1 lung value of 1078 ± 38 ms correlated well with previous reports. Improved intersession variability was observed, as evident from a decreased standard deviation of motion-resolved T1 mapping (F-test = 0.051). Animals received lipopolysaccharide (LPS) and were imaged at t = 2, 6, and 12 h after administration. The nitric oxide (NO)-dependent function was assessed according to changes in lung T1 after L-NAME injection, while microvascular perfusion and oxidant stress were assessed with contrast-enhanced imaging after injection of gadolinium or 3-carbamoyl-proxyl nitroxide radical, respectively. Retrospectivel gated UTE allowed robust, motion-compensated imaging that could be used for T1 mapping of lung parenchyma. Changes in lung T1 after L-NAME injection indicated that LPS induced overproduction of NO at t = 2 and 6 h after LPS, but NO-dependent microvascular function was impaired at t = 12 h after LPS. DynCE imaging at t = 6 h after LPS injection revealed decreased microvascular perfusion, with increased vascular permeability and oxidant stress. MRI allows to visualize and quantify lung microvascular NO-dependent function and its concomitant impairment during acute respiratory distress syndrome development with high sensitivity. UTE T1 mapping appears to be sensitive and useful in probing pulmonary microvascular functional status.
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Affiliation(s)
- Grzegorz Kwiatkowski
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Izabela Czyzynska-Cichon
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Birger Tielemans
- Department of Imaging and Pathology, Biomedical MRI Unit/Molecular Small Animal Imaging Center (MoSAIC), KU Leuven, Leuven, Belgium
| | - Lotte Geerkens
- Department of Imaging and Pathology, Biomedical MRI Unit/Molecular Small Animal Imaging Center (MoSAIC), KU Leuven, Leuven, Belgium
| | - Agnieszka Jasztal
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Greetje Vande Velde
- Department of Imaging and Pathology, Biomedical MRI Unit/Molecular Small Animal Imaging Center (MoSAIC), KU Leuven, Leuven, Belgium
| | - Stefan Chłopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
- Faculty of Medicine, Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
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Niewiadomska-Cimicka A, Fievet L, Surdyka M, Jesion E, Keime C, Singer E, Eisenmann A, Kalinowska-Poska Z, Nguyen HHP, Fiszer A, Figiel M, Trottier Y. AAV-Mediated CAG-Targeting Selectively Reduces Polyglutamine-Expanded Protein and Attenuates Disease Phenotypes in a Spinocerebellar Ataxia Mouse Model. Int J Mol Sci 2024; 25:4354. [PMID: 38673939 DOI: 10.3390/ijms25084354] [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: 03/26/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Polyglutamine (polyQ)-encoding CAG repeat expansions represent a common disease-causing mutation responsible for several dominant spinocerebellar ataxias (SCAs). PolyQ-expanded SCA proteins are toxic for cerebellar neurons, with Purkinje cells (PCs) being the most vulnerable. RNA interference (RNAi) reagents targeting transcripts with expanded CAG reduce the level of various mutant SCA proteins in an allele-selective manner in vitro and represent promising universal tools for treating multiple CAG/polyQ SCAs. However, it remains unclear whether the therapeutic targeting of CAG expansion can be achieved in vivo and if it can ameliorate cerebellar functions. Here, using a mouse model of SCA7 expressing a mutant Atxn7 allele with 140 CAGs, we examined the efficacy of short hairpin RNAs (shRNAs) targeting CAG repeats expressed from PHP.eB adeno-associated virus vectors (AAVs), which were introduced into the brain via intravascular injection. We demonstrated that shRNAs carrying various mismatches with the CAG target sequence reduced the level of polyQ-expanded ATXN7 in the cerebellum, albeit with varying degrees of allele selectivity and safety profile. An shRNA named A4 potently reduced the level of polyQ-expanded ATXN7, with no effect on normal ATXN7 levels and no adverse side effects. Furthermore, A4 shRNA treatment improved a range of motor and behavioral parameters 23 weeks after AAV injection and attenuated the disease burden of PCs by preventing the downregulation of several PC-type-specific genes. Our results show the feasibility of the selective targeting of CAG expansion in the cerebellum using a blood-brain barrier-permeable vector to attenuate the disease phenotype in an SCA mouse model. Our study represents a significant advancement in developing CAG-targeting strategies as a potential therapy for SCA7 and possibly other CAG/polyQ SCAs.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Lorraine Fievet
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Magdalena Surdyka
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Ewelina Jesion
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Céline Keime
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Elisabeth Singer
- Centre for Rare Diseases (ZSE), University of Tuebingen, 72076 Tuebingen, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tuebingen, Germany
- Department of Human Genetics, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany
| | - Aurélie Eisenmann
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Zaneta Kalinowska-Poska
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Hoa Huu Phuc Nguyen
- Department of Human Genetics, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Figiel
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Yvon Trottier
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
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Wiśniewski M, Babirye P, Musubika C, Papakonstantinou E, Kirimunda S, Łaźniewski M, Szczepińska T, Joloba ML, Eliopoulos E, Bongcam-Rudloff E, Vlachakis D, Kumar Halder A, Plewczyński D, Wayengera M. Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies. Brief Funct Genomics 2024:elae012. [PMID: 38605526 DOI: 10.1093/bfgp/elae012] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Intermolecular interactions of protein-protein complexes play a principal role in the process of discovering new substances used in the diagnosis and treatment of many diseases. Among such complexes of proteins, we have to mention antibodies; they interact with specific antigens of two genera of single-stranded RNA viruses belonging to the family Filoviridae-Ebolavirus and Marburgvirus; both cause rare but fatal viral hemorrhagic fever in Africa, with pandemic potential. In this research, we conduct studies aimed at the design and evaluation of antibodies targeting the filovirus glycoprotein precursor GP-1,2 to develop potential targets for the pan-filovirus easy-to-use rapid diagnostic tests. The in silico research using the available 3D structure of the natural antibody-antigen complex was carried out to determine the stability of individual protein segments in the process of its formation and maintenance. The computed free binding energy of the complex and its decomposition for all amino acids allowed us to define the residues that play an essential role in the structure and indicated the spots where potential antibodies can be improved. Following that, the study involved targeting six epitopes of the filovirus GP1,2 with two polyclonal antibodies (pABs) and 14 monoclonal antibodies (mABs). The evaluation conducted using Enzyme Immunoassays tested 62 different sandwich combinations of monoclonal antibodies (mAbs), identifying 10 combinations that successfully captured the recombinant GP1,2 (rGP). Among these combinations, the sandwich option (3G2G12* - (rGP) - 2D8F11) exhibited the highest propensity for capturing the rGP antigen.
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Affiliation(s)
- Maciej Wiśniewski
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Peace Babirye
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Carol Musubika
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Eleni Papakonstantinou
- Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology,Agricultural University of Athens, Iera Odos 7511855 Athens, Greece
| | - Samuel Kirimunda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Michal Łaźniewski
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Teresa Szczepińska
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Elias Eliopoulos
- Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology,Agricultural University of Athens, Iera Odos 7511855 Athens, Greece
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics section, Swedish University for Agricultural Sciences, Ulls väg 26, PO Box 7023, S-750 07 Uppsala, Sweden
| | - Dimitrios Vlachakis
- Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology, Agricultural University of Athens, Iera Odos 7511855 Athens, Greece
| | - Anup Kumar Halder
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Dariusz Plewczyński
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
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Kimsa-Dudek M, Kruszniewska-Rajs C, Adamska J, Strzałka-Mrozik B, Matwijczuk A, Karcz D, Gagoś M, Gola JM. Redox homeostasis in human renal cells that had been treated with amphotericin B in combination with selected 1,3,4-thiadiazole derivatives. Pharmacol Rep 2024:10.1007/s43440-024-00592-7. [PMID: 38587587 DOI: 10.1007/s43440-024-00592-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND The use of amphotericin B (AmB) in the therapy of systemic mycosis is associated with strong side effects, including nephrotoxicity, and hepatotoxicity. Therefore, agents that can reduce the toxic effects of AmB while acting synergistically as antifungal agents are currently being sought. 1,3,4-thiadiazole derivatives are promising compounds that have an antifungal activity and act synergically with AmB. Such combinations might allow the dose of AmB, which is essential for preventing patients from having serious side effects, to be decreased. This might result from the antioxidant properties of 1,3,4-thiadiazoles. Thus, the aim of the study was to investigate redox homeostasis in human renal proximal tubule epithelial cells (RPTEC) after they had been treated with AmB in combination with 1,3,4-thiadiazole derivatives. METHODS Cellular redox homeostasis was assessed by investigating the total antioxidant capacity (TAC) of cells, the malondialdehyde (MDA) concentration, and the activity of antioxidant enzymes such as superoxide dismutase (SOD), glutathione peroxidase (GPX), and catalase (CAT). TAC was measured using an ABTS method. The MDA concentration, and the activity of SOD, GPX, and CAT were determined spectrophotometrically using commercially available assays. Additionally, the antioxidant defense system-related gene expression profile was determined using oligonucleotide microarrays (HG-U133A 2.0). Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to confirm the microarray results. RESULTS Amphotericin B and selected 1,3,4-thiadiazole derivatives had a significant effect on the total antioxidant capacity of the RPTEC cells, and the activity of the antioxidant enzymes. We also revealed that the effect of thiadiazoles on the SOD and CAT activities is dependent on the treatment of RPTEC cells with AmB. At the transcriptional level, the expression of several genes was affected by the studied compounds and their combinations. CONCLUSIONS The results confirmed that thiadiazoles can stimulate the RPTEC cells to defend against the oxidative stress that is generated by AmB. In addition, together with the previously demonstrated synergistic antifungal activity, and low nephrotoxicity, these compounds have the potential to be used in new therapeutic strategies in the treatment of fungal infections.
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Affiliation(s)
- Magdalena Kimsa-Dudek
- Department of Nutrigenomics, and Bromatology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland.
| | - Celina Kruszniewska-Rajs
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
| | - Jolanta Adamska
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
| | - Barbara Strzałka-Mrozik
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
| | - Arkadiusz Matwijczuk
- Department of Biophysics, University of Life Sciences, Akademicka 13, Lublin, 20-950, Poland
- ECOTECH-COMPLEX-Analytical, and Programme Centre for Advanced Environmentally- Friendly Technologies, Maria Curie-Sklodowska University, Głęboka 39, Lublin, 20-033, Poland
| | - Dariusz Karcz
- Department of Chemical Technology, and Environmental Analytics, Cracow University of Technology, Cracow, 31-155, Poland
- ECOTECH-COMPLEX-Analytical, and Programme Centre for Advanced Environmentally- Friendly Technologies, Maria Curie-Sklodowska University, Głęboka 39, Lublin, 20-033, Poland
| | - Mariusz Gagoś
- Department of Cell Biology, Maria Curie-Sklodowska University, Akademicka 19, Lublin, 20-033, Poland
- Department of Biochemistry, and Molecular Biology, Medical University of Lublin, Lublin, 20-093, Poland
| | - Joanna Magdalena Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
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Banasiewicz M, Deperasińska I, Gawryś P, Suwińska K, Kozankiewicz B. 2,3-Dichloroanthracene crystal, a new rigid matrix for single molecule optical investigations. Chemphyschem 2024; 25:e202300668. [PMID: 38282140 DOI: 10.1002/cphc.202300668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Absorption and emission spectra of single crystals of 2,3-dichloroathracene (23DCA) and 23DCA dispersed in n-nonane matrix were studied at 5 K. Singlet and triplet excitonic bands in the crystal were estimated to be at about 415 nm and at wavelengths shorter than 700 nm, respectively. Thus, from the spectroscopic point of view, these crystals satisfy all criteria for a transparent and rigid matrix for low temperature optical studies of single molecules of dibenzoterrylene, which have their purely electronic S0→S1 transition at around 785 nm. Quantum-chemistry calculations were used to analyze the spectra.
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Affiliation(s)
- Marzena Banasiewicz
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668, Warsaw, Poland
| | - Irena Deperasińska
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668, Warsaw, Poland
| | - Paweł Gawryś
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668, Warsaw, Poland
| | - Kinga Suwińska
- Cardinal Stefan Wyszyński University in Warsaw, Faculty of Mathematics and Natural Sciences, K. Wóycickiego 1/3, 01-938, Warsaw, Poland
| | - Bolesław Kozankiewicz
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668, Warsaw, Poland
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Sivaraman K, Liu B, Martinez-Delgado B, Held J, Büttner M, Illig T, Volland S, Gomez-Mariano G, Jedicke N, Yevsa T, Welte T, DeLuca DS, Wrenger S, Olejnicka B, Janciauskiene S. Human Bronchial Epithelial Cell Transcriptome Changes in Response to Serum from Patients with Different Status of Inflammation. Lung 2024; 202:157-170. [PMID: 38494528 PMCID: PMC11009779 DOI: 10.1007/s00408-024-00679-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/02/2024] [Indexed: 03/19/2024]
Abstract
PURPOSE To investigate the transcriptome of human bronchial epithelial cells (HBEC) in response to serum from patients with different degrees of inflammation. METHODS Serum from 19 COVID-19 patients obtained from the Hannover Unified Biobank was used. At the time of sampling, 5 patients had a WHO Clinical Progression Scale (WHO-CPS) score of 9 (severe illness). The remaining 14 patients had a WHO-CPS of below 9 (range 1-7), and lower illness. Multiplex immunoassay was used to assess serum inflammatory markers. The culture medium of HBEC was supplemented with 2% of the patient's serum, and the cells were cultured at 37 °C, 5% CO2 for 18 h. Subsequently, cellular RNA was used for RNA-Seq. RESULTS Patients with scores below 9 had significantly lower albumin and serum levels of E-selectin, IL-8, and MCP-1 than patients with scores of 9. Principal component analysis based on 500 "core genes" of RNA-seq segregated cells into two subsets: exposed to serum from 4 (I) and 15 (II) patients. Cells from a subset (I) treated with serum from 4 patients with a score of 9 showed 5566 differentially expressed genes of which 2793 were up- and 2773 downregulated in comparison with cells of subset II treated with serum from 14 patients with scores between 1 and 7 and one with score = 9. In subset I cells, a higher expression of TLR4 and CXCL8 but a lower CDH1, ACE2, and HMOX1, and greater effects on genes involved in metabolic regulation, cytoskeletal organization, and kinase activity pathways were observed. CONCLUSION This simple model could be useful to characterize patient serum and epithelial cell properties.
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Affiliation(s)
- Kokilavani Sivaraman
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - Bin Liu
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - Beatriz Martinez-Delgado
- Department of Molecular Genetics, Institute of Health Carlos III, Institute for Rare Diseases Research, CIBER of Rare Diseases (CIBERER), Majadahonda, 28220, Madrid, Spain
| | - Julia Held
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - Manuela Büttner
- Hannover Medical School, Central Animal Facility, Hannover, Germany
| | - Thomas Illig
- Hannover Medical School, Hannover Unified Biobank, Hannover, Germany
| | - Sonja Volland
- Hannover Medical School, Hannover Unified Biobank, Hannover, Germany
| | - Gema Gomez-Mariano
- Department of Molecular Genetics, Institute of Health Carlos III, Institute for Rare Diseases Research, CIBER of Rare Diseases (CIBERER), Majadahonda, 28220, Madrid, Spain
| | - Nils Jedicke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Tetyana Yevsa
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - David S DeLuca
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - Sabine Wrenger
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - Beata Olejnicka
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany
| | - Sabina Janciauskiene
- Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL), Feodor-Lynen-Str. 23, 30625, Hannover, Germany.
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Zhang D, Czapinska H, Bochtler M, Wlodawer A, Lubkowski J. RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases. Protein Sci 2024; 33:e4920. [PMID: 38501449 PMCID: PMC10949315 DOI: 10.1002/pro.4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024]
Abstract
L-Asparaginases (ASNases) catalyze the hydrolysis of L-Asn to L-Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300-400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum, reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N-terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L-Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short-chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild-type RrA, both with and without bound L-Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand-alone subfamily of ASNases that can catalyze the hydrolysis of L-Asn to L-Asp despite the lack of the C-terminal domain that is present in all ASNases described structurally to date.
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Affiliation(s)
- Di Zhang
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Honorata Czapinska
- Laboratory of Structural BiologyInternational Institute of Molecular and Cell BiologyWarsawPoland
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Matthias Bochtler
- Laboratory of Structural BiologyInternational Institute of Molecular and Cell BiologyWarsawPoland
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Alexander Wlodawer
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Jacek Lubkowski
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
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Drobniak SM, Lagisz M, Yang Y, Nakagawa S. Realism and robustness require increased sample size when studying both sexes. PLoS Biol 2024; 22:e3002456. [PMID: 38603525 PMCID: PMC11008793 DOI: 10.1371/journal.pbio.3002456] [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: 12/01/2023] [Indexed: 04/13/2024] Open
Abstract
A recent article claimed that researchers need not increase the overall sample size for a study that includes both sexes. This Formal Comment points out that that study assumed two sexes to have the same variance, and explains why this is a unrealistic assumption.
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Affiliation(s)
- Szymon M. Drobniak
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Yefeng Yang
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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Wielkopolan B, Szabelska‐Beręsewicz A, Gawor J, Obrępalska‐Stęplowska A. Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action. Environ Microbiol Rep 2024; 16:e13247. [PMID: 38644048 PMCID: PMC11033208 DOI: 10.1111/1758-2229.13247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/12/2024] [Indexed: 04/23/2024]
Abstract
The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.
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Affiliation(s)
- Beata Wielkopolan
- Department of Monitoring and Signaling of AgrophagesInstitute of Plant Protection–National Research InstitutePoznanPoland
| | | | - Jan Gawor
- DNA Sequencing and Synthesis FacilityInstitute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
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10
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Kumar Halder A, Agarwal A, Jodkowska K, Plewczynski D. A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction. Brief Funct Genomics 2024:elae009. [PMID: 38555493 DOI: 10.1093/bfgp/elae009] [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: 11/28/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
Genomic data analysis has witnessed a surge in complexity and volume, primarily driven by the advent of high-throughput technologies. In particular, studying chromatin loops and structures has become pivotal in understanding gene regulation and genome organization. This systematic investigation explores the realm of specialized bioinformatics pipelines designed specifically for the analysis of chromatin loops and structures. Our investigation incorporates two protein (CTCF and Cohesin) factor-specific loop interaction datasets from six distinct pipelines, amassing a comprehensive collection of 36 diverse datasets. Through a meticulous review of existing literature, we offer a holistic perspective on the methodologies, tools and algorithms underpinning the analysis of this multifaceted genomic feature. We illuminate the vast array of approaches deployed, encompassing pivotal aspects such as data preparation pipeline, preprocessing, statistical features and modelling techniques. Beyond this, we rigorously assess the strengths and limitations inherent in these bioinformatics pipelines, shedding light on the interplay between data quality and the performance of deep learning models, ultimately advancing our comprehension of genomic intricacies.
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Affiliation(s)
- Anup Kumar Halder
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Abhishek Agarwal
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Karolina Jodkowska
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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11
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Kusak R, Nasiadek M, Stragierowicz J, Hanke W, Kilanowicz A. Changes in Endogenous Essential Metal Homeostasis in the Liver and Kidneys during a Six-Month Follow-Up Period after Subchronic Cadmium Exposure. Int J Mol Sci 2024; 25:3829. [PMID: 38612636 PMCID: PMC11011286 DOI: 10.3390/ijms25073829] [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: 02/23/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Cadmium (Cd) is one of the most dangerous environmental pollutants. Its mechanism of action is multidirectional; among other things, it disrupts the balance of key essential elements. The aim of this study was to assess how cumulative exposure to Cd influences its interaction with selected essential elements (Cu, Zn, Ca, and Mg) in the kidney and liver during long-term observation (90 and 180 days) after subchronic exposure of rats (90 days) to Cd at common environmental (0.09 and 0.9 mg Cd/kg b.w.) and higher (1.8 and 4.5 mg Cd/kg b.w.) doses. Cd and essential elements were analyzed using the F-AAS and GF-AAS techniques. It was shown that the highest bioaccumulation of Cd in the kidney occurred six months after the end of exposure, and importantly, the highest accumulation was found after the lowest Cd dose (i.e., environmental exposure). Organ bioaccumulation of Cd (>21 μgCd/g w.w. in the kidney and >6 μgCd/g w.w. in the liver) was accompanied by changes in the other studied essential elements, particularly Cu in both the kidney and liver and Zn in the liver; these persisted for as long as six months after the end of the exposure. The results suggest that the critical concentration in human kidneys (40 μgCd/g w.w.), currently considered safe, may be too high and should be reviewed, as the observed long-term imbalance of Cu/Zn in the kidneys may lead to renal dysfunction.
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Affiliation(s)
- Rafał Kusak
- Medical Centers the Medici, 91-053 Lodz, Poland
| | - Marzenna Nasiadek
- Department of Toxicology, Medical University of Lodz, 90-151 Lodz, Poland; (J.S.); (A.K.)
| | - Joanna Stragierowicz
- Department of Toxicology, Medical University of Lodz, 90-151 Lodz, Poland; (J.S.); (A.K.)
| | - Wojciech Hanke
- Medical Informatics and Statistics Department, Medical University of Lodz, 90-419 Lodz, Poland;
| | - Anna Kilanowicz
- Department of Toxicology, Medical University of Lodz, 90-151 Lodz, Poland; (J.S.); (A.K.)
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12
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Efentakis P, Choustoulaki A, Kwiatkowski G, Varela A, Kostopoulos IV, Tsekenis G, Ntanasis-Stathopoulos I, Georgoulis A, Vorgias CE, Gakiopoulou H, Briasoulis A, Davos CH, Kostomitsopoulos N, Tsitsilonis O, Dimopoulos MA, Terpos E, Chłopicki S, Gavriatopoulou M, Andreadou I. Early microvascular coronary endothelial dysfunction precedes pembrolizumab-induced cardiotoxicity. Preventive role of high dose of atorvastatin. Basic Res Cardiol 2024:10.1007/s00395-024-01046-0. [PMID: 38520533 DOI: 10.1007/s00395-024-01046-0] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/25/2024]
Abstract
Immune checkpoint inhibitors (ICIs) exhibit remarkable antitumor activity and immune-related cardiotoxicity of unknown pathomechanism. The aim of the study was to investigate the ICI class-dependent cardiotoxicity in vitro and pembrolizumab's (Pem's) cardiotoxicity in vivo, seeking for translational prevention means. Cytotoxicity was investigated in primary cardiomyocytes and splenocytes, incubated with ipilimumab, Pem and avelumab. Pem's cross-reactivity was assessed by circular dichroism (CD) on biotechnologically produced human and murine PD-1 and in silico. C57BL6/J male mice received IgG4 or Pem for 2 and 5 weeks. Echocardiography, histology, and molecular analyses were performed. Coronary blood flow velocity mapping and cardiac magnetic resonance imaging were conducted at 2 weeks. Human EA.hy926 endothelial cells were incubated with Pem-conditioned media from human mononuclear cells, in presence and absence of statins and viability and molecular signaling were assessed. Atorvastatin (20 mg/kg, daily) was administered in vivo, as prophylaxis. Only Pem exerted immune-related cytotoxicity in vitro. Pem's cross-reactivity with the murine PD-1 was confirmed by CD and docking. In vivo, Pem initiated coronary endothelial and diastolic dysfunction at 2 weeks and systolic dysfunction at 5 weeks. At 2 weeks, Pem induced ICAM-1 and iNOS expression and intracardiac leukocyte infiltration. At 5 weeks, Pem exacerbated endothelial activation and triggered cardiac inflammation. Pem led to immune-related cytotoxicity in EA.hy926 cells, which was prevented by atorvastatin. Atorvastatin mitigated functional deficits, by inhibiting endothelial dysfunction in vivo. We established for the first time an in vivo model of Pem-induced cardiotoxicity. Coronary endothelial dysfunction precedes Pem-induced cardiotoxicity, whereas atorvastatin emerges as a novel prophylactic therapy.
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Affiliation(s)
- Panagiotis Efentakis
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Angeliki Choustoulaki
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Grzegorz Kwiatkowski
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Kraków, Poland
| | - Aimilia Varela
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Ioannis V Kostopoulos
- Flow Cytometry Unit, Section of Animal and Human Physiology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - George Tsekenis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Ioannis Ntanasis-Stathopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasios Georgoulis
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Constantinos E Vorgias
- Department of Biochemistry & Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Harikleia Gakiopoulou
- Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Briasoulis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Ourania Tsitsilonis
- Flow Cytometry Unit, Section of Animal and Human Physiology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Stefan Chłopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Kraków, Poland
- Medical College, Jagiellonian University, Krakow, Poland
| | - Maria Gavriatopoulou
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece.
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13
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Kokot A, Gadakh S, Saha I, Gajda E, Łaźniewski M, Rakshit S, Sengupta K, Mollah AF, Denkiewicz M, Górczak K, Claesen J, Burzykowski T, Plewczynski D. Unveiling the Molecular Mechanism of Trastuzumab Resistance in SKBR3 and BT474 Cell Lines for HER2 Positive Breast Cancer. Curr Issues Mol Biol 2024; 46:2713-2740. [PMID: 38534787 DOI: 10.3390/cimb46030171] [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: 01/25/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024] Open
Abstract
HER2-positive breast cancer is one of the most prevalent forms of cancer among women worldwide. Generally, the molecular characteristics of this breast cancer include activation of human epidermal growth factor receptor-2 (HER2) and hormone receptor activation. HER2-positive is associated with a higher death rate, which led to the development of a monoclonal antibody called trastuzumab, specifically targeting HER2. The success rate of HER2-positive breast cancer treatment has been increased; however, drug resistance remains a challenge. This fact motivated us to explore the underlying molecular mechanisms of trastuzumab resistance. For this purpose, a two-fold approach was taken by considering well-known breast cancer cell lines SKBR3 and BT474. In the first fold, trastuzumab treatment doses were optimized separately for both cell lines. This was done based on the proliferation rate of cells in response to a wide variety of medication dosages. Thereafter, each cell line was cultivated with a steady dosage of herceptin for several months. During this period, six time points were selected for further in vitro analysis, ranging from the untreated cell line at the beginning to a fully resistant cell line at the end of the experiment. In the second fold, nucleic acids were extracted for further high throughput-based microarray experiments of gene and microRNA expression. Such expression data were further analyzed in order to infer the molecular mechanisms involved in the underlying development of trastuzumab resistance. In the list of differentially expressed genes and miRNAs, multiple genes (e.g., BIRC5, E2F1, TFRC, and USP1) and miRNAs (e.g., hsa miR 574 3p, hsa miR 4530, and hsa miR 197 3p) responsible for trastuzumab resistance were found. Downstream analysis showed that TFRC, E2F1, and USP1 were also targeted by hsa-miR-8485. Moreover, it indicated that miR-4701-5p was highly expressed as compared to TFRC in the SKBR3 cell line. These results unveil key genes and miRNAs as molecular regulators for trastuzumab resistance.
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Affiliation(s)
- Anna Kokot
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Sachin Gadakh
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Indrajit Saha
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata 700106, India
| | - Ewa Gajda
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Michał Łaźniewski
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Somnath Rakshit
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Kaustav Sengupta
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warszawa, Poland
| | | | - Michał Denkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Katarzyna Górczak
- Department of Mathematics and Statistics, Hasselt University, 3500 Hasselt, Belgium
| | - Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam Universitair Medische Centra, VU University, 1081 HV Amsterdam, The Netherlands
| | - Tomasz Burzykowski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
- Department of Mathematics and Statistics, Hasselt University, 3500 Hasselt, Belgium
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14
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Suszynska M, Machowska M, Fraszczyk E, Michalczyk M, Philips A, Galka-Marciniak P, Kozlowski P. CMC: Cancer miRNA Census - a list of cancer-related miRNA genes. Nucleic Acids Res 2024; 52:1628-1644. [PMID: 38261968 PMCID: PMC10899758 DOI: 10.1093/nar/gkae017] [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: 06/26/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
A growing body of evidence indicates an important role of miRNAs in cancer; however, there is no definitive, convenient-to-use list of cancer-related miRNAs or miRNA genes that may serve as a reference for analyses of miRNAs in cancer. To this end, we created a list of 165 cancer-related miRNA genes called the Cancer miRNA Census (CMC). The list is based on a score, built on various types of functional and genetic evidence for the role of particular miRNAs in cancer, e.g. miRNA-cancer associations reported in databases, associations of miRNAs with cancer hallmarks, or signals of positive selection of genetic alterations in cancer. The presence of well-recognized cancer-related miRNA genes, such as MIR21, MIR155, MIR15A, MIR17 or MIRLET7s, at the top of the CMC ranking directly confirms the accuracy and robustness of the list. Additionally, to verify and indicate the reliability of CMC, we performed a validation of criteria used to build CMC, comparison of CMC with various cancer data (publications and databases), and enrichment analyses of biological pathways and processes such as Gene Ontology or DisGeNET. All validation steps showed a strong association of CMC with cancer/cancer-related processes confirming its usefulness as a reference list of miRNA genes associated with cancer.
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Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Magdalena Machowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Eliza Fraszczyk
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Maciej Michalczyk
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
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15
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Niśkiewicz M, Szymański P, Zampa L, Budka M, Osiejuk TS. Neighbour-stranger discrimination in an African wood dove inhabiting equatorial rainforest. Sci Rep 2024; 14:4252. [PMID: 38378955 PMCID: PMC10879109 DOI: 10.1038/s41598-024-53867-7] [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: 09/28/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
We investigated within- and between-individual song variation and song-based neighbour-stranger discrimination in a non-learning bird species, the blue-headed wood-dove (Turtur brehmeri), which inhabits lowland rainforests of West and Central Africa. We found that songs of this species are individually specific and have a high potential for use in individual recognition based on the time-frequency pattern of note distribution within song phrases. To test whether these differences affect behaviour, we conducted playback experiments with 19 territorial males. Each male was tested twice, once with the songs of a familiar neighbour and once with the songs of an unfamiliar stranger. We observed that males responded more aggressively to playback of a stranger's songs: they quickly approached close to the speaker and spent more time near it. However, no significant differences between treatments were observed in the vocal responses. In addition, we explored whether responses differed based on the song frequency of the focal male and/or that of the simulated intruder (i.e., playback), as this song parameter is inversely related to body size and could potentially affect males' decisions to respond to other birds. Song frequency parameters (of either the focal male or the simulated intruder) had no effect on the approaching response during playback. However, we found that the pattern of response after playback was significantly affected by the song frequency of the focal male: males with lower-frequency songs stayed closer to the simulated intruder for a longer period of time without singing, while males with higher-frequency songs returned more quickly to their initial song posts and resumed singing. Together, these results depict a consistently strong response to strangers during and after playback that is dependent on a male's self-assessment rather than assessment of a rival's strength based on his song frequency. This work provides the first experimental evidence that doves (Columbidae) can use songs for neighbour-stranger discrimination and respond according to a "dear enemy" scheme that keeps the cost of territory defence at a reasonable level.
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Affiliation(s)
- Małgorzata Niśkiewicz
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Paweł Szymański
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Lia Zampa
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Michał Budka
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Tomasz S Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Nagaraj S, Stankiewicz-Drogon A, Darzynkiewicz E, Wojda U, Grzela R. miR-483-5p orchestrates the initiation of protein synthesis by facilitating the decrease in phosphorylated Ser209eIF4E and 4E-BP1 levels. Sci Rep 2024; 14:4237. [PMID: 38378793 PMCID: PMC10879198 DOI: 10.1038/s41598-024-54154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Eukaryotic initiation factor 4E (eIF4E) is a pivotal protein involved in the regulatory mechanism for global protein synthesis in both physiological and pathological conditions. MicroRNAs (miRNAs) play a significant role in regulating gene expression by targeting mRNA. However, the ability of miRNAs to regulate eIF4E and its phosphorylation remains relatively unknown. In this study, we predicted and experimentally verified targets for miR-483-5p, including eukaryotic translation initiation factor eIF4E and its binding proteins, 4E-BPs, that regulate protein synthesis. Using the Web of Science database, we identified 28 experimentally verified miR-483-5p targets, and by the TargetScan database, we found 1818 predicted mRNA targets, including EIF4E, EIF4EBP1, and EIF4EBP2. We verified that miR-483-5p significantly reduced ERK1 and MKNK1 mRNA levels in HEK293 cells. Furthermore, we discovered that miR-483-5p suppressed EIF4EBP1 and EIF4EBP2, but not EIF4E. Finally, we found that miR-483-5p reduced the level of phosphorylated eIF4E (pSer209eIF4E) but not total eIF4E. In conclusion, our study suggests that miR-483-5p's multi-targeting effect on the ERK1/ MKNK1 axis modulates the phosphorylation state of eIF4E. Unlike siRNA, miRNA can have multiple targets in the pathway, and thereby exploring the role of miR-483-5p in various cancer models may uncover therapeutic options.
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Affiliation(s)
- Siranjeevi Nagaraj
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093, Warsaw, Poland
| | - Anna Stankiewicz-Drogon
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093, Warsaw, Poland.
| | - Renata Grzela
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
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17
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Carballo-Casla A, Stefler D, Ortolá R, Chen Y, Knuppel A, Kubinova R, Pajak A, Rodríguez-Artalejo F, Brunner EJ, Bobak M. The Southern European Atlantic diet and all-cause and cause-specific mortality: a European multicohort study. Eur J Prev Cardiol 2024; 31:358-367. [PMID: 38102063 PMCID: PMC10873144 DOI: 10.1093/eurjpc/zwad370] [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: 10/11/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 12/17/2023]
Abstract
AIMS The Southern European Atlantic diet (SEAD) is the traditional dietary pattern of northwestern Spain and northern Portugal, but it may resemble that of central, eastern, and western European countries. The SEAD has been found associated with lower risk of myocardial infarction and mortality in older adults, but it is uncertain whether this association also exists in other European populations and if it is similar as that found in its countries of origin. METHODS AND RESULTS We conducted a prospective analysis of four cohorts with 35 917 subjects aged 18-96 years: ENRICA (Spain), HAPIEE (Czechia and Poland), and Whitehall II (United Kingdom). The SEAD comprised fresh fish, cod, red meat and pork products, dairy, legumes and vegetables, vegetable soup, potatoes, whole-grain bread, and moderate wine consumption. Associations were adjusted for sociodemographic variables, energy intake, lifestyle, and morbidity. After a median follow-up of 13.6 years (range = 0-15), we recorded 4 973 all-cause, 1 581 cardiovascular, and 1 814 cancer deaths. Higher adherence to the SEAD was associated with lower mortality in the pooled sample. Fully adjusted hazard ratios and 95% confidence interval per 1-standard deviation increment in the SEAD were 0.92 (0.89, 0.95), 0.91 (0.86, 0.96), and 0.94 (0.89, 0.99) for all-cause, cardiovascular, and cancer mortality, respectively. The association of the SEAD with all-cause mortality was not significantly different between countries [Spain = 0.93 (0.88, 0.99), Czechia = 0.94 (0.89,0.99), Poland = 0.89 (0.85, 0.93), United Kingdom = 0.98 (0.89, 1.07); P for interaction = 0.16]. CONCLUSION The SEAD was associated with lower all-cause, cardiovascular, and cancer mortality in southern, central, eastern, and western European populations. Associations were of similar magnitude as those found for existing healthy dietary patterns.
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Affiliation(s)
- Adrián Carballo-Casla
- Department of Preventive Medicine and Public Health, Universidad Autónoma de Madrid, Calle del Arzobispo Morcillo 4, 28029 Madrid, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBERESP), Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 7HB, UK
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet & Stockholm University, Tomtebodavägen 18 A SE-171 77 Stockholm, Sweden
| | - Denes Stefler
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 7HB, UK
| | - Rosario Ortolá
- Department of Preventive Medicine and Public Health, Universidad Autónoma de Madrid, Calle del Arzobispo Morcillo 4, 28029 Madrid, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBERESP), Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Yuntao Chen
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 7HB, UK
| | | | - Ruzena Kubinova
- Department of Environmental Health and Population Health Monitoring, National Institute of Public Health, Šrobárova 49/48, 100 00 Prague, Czech Republic
| | - Andrzej Pajak
- Department of Epidemiology and Population Studies, Faculty of Health Sciences, Institute of Public Health, Jagiellonian University Medical College, Ulica Skawińska 8, 31-066 Krakow, Poland
| | - Fernando Rodríguez-Artalejo
- Department of Preventive Medicine and Public Health, Universidad Autónoma de Madrid, Calle del Arzobispo Morcillo 4, 28029 Madrid, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBERESP), Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
- Cardiovascular and Nutritional Epidemiology Group, CEI UAM+CSIC, IMDEA Research Institute on Food & Health Sciences, Carretera de Canto Blanco 8, 28049 Madrid, Spain
| | - Eric J Brunner
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 7HB, UK
| | - Martin Bobak
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 7HB, UK
- RECETOX, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
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18
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Le Garff P, Maria Losus R, Chaudhary S, Dobrzańska L. Tailoring the dimensionality of metal complexes via ligand modifications. Acta Crystallogr B Struct Sci Cryst Eng Mater 2024; 80:19-26. [PMID: 38205838 DOI: 10.1107/s2052520623010260] [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: 09/15/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
A series of CuII complexes obtained under the same reaction conditions has been analyzed to gain insight into the effect of the ligand composition on the final reaction product. Dipodal ligands containing N-donor imidazole rings and a benzene ring as a spacer with different numbers of methyl substituents on the aromatic rings were selected for the study such as 1,3-bis(imidazol-1-ylmethyl)benzene (L1), 1,3-bis(imidazol-1-ylmethyl)-5-methylbenzene (L2), 1,3-bis(imidazol-1-ylmethyl)-2,4,6-trimethylbenzene (L3), 1,3-bis(2-methylimidazol-1-ylmethyl)-2,4,6-trimethylbenzene (L4). L4 has not been reported previously and was synthesized for this study. The formed metal complexes show the presence of polymeric (ligand with no or one methyl substituent; 1-4), or discrete motifs (3- or 5-methyl substituents; 5-7). The new metal complexes 3, 5 and 6 were analyzed using single-crystal X-ray diffraction and powder diffraction. In addition, the structural analyses were supported by computational methods.
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Affiliation(s)
- Paul Le Garff
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, Toruń, 87-100, Poland
| | - Renny Maria Losus
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, Toruń, 87-100, Poland
| | - Simran Chaudhary
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, Toruń, 87-100, Poland
| | - Liliana Dobrzańska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, Toruń, 87-100, Poland
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19
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Golec de Zavala A, Keenan O, Ziegler M, Ciesielski P, Wahl JE, Mazurkiewicz M. App-based mindfulness training supported eudaimonic wellbeing during the COVID19 pandemic. Appl Psychol Health Well Being 2024; 16:42-59. [PMID: 37432062 DOI: 10.1111/aphw.12468] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023]
Abstract
A randomized-controlled-trial study (N = 219) tested two pre-registered hypotheses that mobile-phone app-based mindfulness training improves wellbeing and increases self-transcendent emotions: gratitude, self-compassion, and awe. Latent change score modeling with a robust maximum likelihood estimator was used to test how those changes are associated in the training versus the waiting-list group. The training increased wellbeing and all self-transcendent emotions regardless of interindividual variance in the changes across time. Changes in all self-transcendent emotions were positively associated with changes in wellbeing. The strength of those associations was comparable in the waiting-list group and the training group. More studies are needed to test whether the effects of mindfulness practice on wellbeing are driven by increases in self-transcendent emotions. The study was conducted over 6 weeks during the COVID19 pandemic. The results indicate that the mindfulness training can be an easily accessible effective intervention supporting eudaimonic wellbeing in face of adversity.
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Affiliation(s)
| | | | | | | | - Julia E Wahl
- SWPS University of Social Sciences and Humanities, Poznań, Poland
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20
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Karbowska M, Pawlak K, Sieklucka B, Domaniewski T, Lebkowska U, Zawadzki R, Pawlak D. Dose-dependent exposure to indoxyl sulfate alters AHR signaling, sirtuins gene expression, oxidative DNA damage, and bone mineral status in rats. Sci Rep 2024; 14:2583. [PMID: 38297036 PMCID: PMC10831046 DOI: 10.1038/s41598-024-53164-3] [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: 07/03/2023] [Accepted: 01/29/2024] [Indexed: 02/02/2024] Open
Abstract
Indoxyl sulfate (IS), an agonist of aryl hydrocarbon receptors (AhR), can accumulate in patients with chronic kidney disease, but its direct effect on bone is not clear. The present study investigated the effect of chronic exposure to low (100 mg/kg b.w.; 100 IS) and high (200 mg/kg b.w.; 200 IS) dose of IS on bone AhR pathway, sirtuins (SIRTs) expression, oxidative DNA damage and bone mineral status in Wistar rats. The accumulation of IS was observed only in trabecular bone tissue in both doses. The differences were observed in the bone parameters, depending on the applied IS dose. The exposure to 100 IS increased AhR repressor (AhRR)-CYP1A2 gene expression, which was associated with SIRT-1, SIRT-3 and SIRT-7 expression. At the low dose group, the oxidative DNA damage marker was unchanged in the bone samples, and it was inversely related to the abovementioned SIRTs expression. In contrast, the exposure to 200 IS reduced the expression of AhRR, CYP1A, SIRT-3 and SIRT-7 genes compared to 100 IS. The level of oxidative DNA damage was higher in trabecular bone in 200 IS group. Femoral bone mineral density was decreased, and inverse relations were noticed between the level of trabecular oxidative DNA damage and parameters of bone mineral status. In conclusion, IS modulates AhR-depending signaling affecting SIRTs expression, oxidative DNA damage and bone mineral status in a dose dependent manner.
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Affiliation(s)
- Malgorzata Karbowska
- Department of Pharmacodynamics, Medical University of Bialystok, Białystok, Poland.
| | - Krystyna Pawlak
- Department of Monitored Pharmacotherapy, Medical University of Bialystok, Białystok, Poland
| | - Beata Sieklucka
- Department of Pharmacodynamics, Medical University of Bialystok, Białystok, Poland
| | - Tomasz Domaniewski
- Department of Monitored Pharmacotherapy, Medical University of Bialystok, Białystok, Poland
| | - Urszula Lebkowska
- Department of Radiology, Medical University of Bialystok, Białystok, Poland
| | - Radoslaw Zawadzki
- Department of Radiology, Medical University of Bialystok, Białystok, Poland
| | - Dariusz Pawlak
- Department of Pharmacodynamics, Medical University of Bialystok, Białystok, Poland
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21
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Durka P, Dovgialo M, Duszyk-Bogorodzka A, Biegański P. Two-Stage Atomic Decomposition of Multichannel EEG and the Previously Undetectable Sleep Spindles. Sensors (Basel) 2024; 24:842. [PMID: 38339559 PMCID: PMC10856903 DOI: 10.3390/s24030842] [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: 12/27/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
We propose a two-step procedure for atomic decomposition of multichannel EEGs, based upon multivariate matching pursuit and dipolar inverse solution, from which atoms representing relevant EEG structures are selected according to prior knowledge. We detect sleep spindles in 147 polysomnographic recordings from the Montreal Archive of Sleep Studies. Detection is compared with human scorers and two state-of-the-art algorithms, which find only about a third of the structures conforming to the definition of sleep spindles and detected by the proposed method. We provide arguments supporting the thesis that the previously undetectable sleep spindles share the same properties as those marked by human experts and previously applied methods, and were previously omitted only because of unfavorable local signal-to-noise ratios, obscuring their visibility to both human experts and algorithms replicating their markings. All detected EEG structures are automatically parametrized by their time and frequency centers, width duration, phase, and spatial location of an equivalent dipolar source within the brain. It allowed us, for the first time, to estimate the spatial gradient of sleep spindles frequencies, which not only confirmed quantitatively the well-known prevalence of higher frequencies in posterior regions, but also revealed a significant gradient in the sagittal plane. The software used in this study is freely available.
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Affiliation(s)
- Piotr Durka
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (M.D.); (P.B.)
| | - Marian Dovgialo
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (M.D.); (P.B.)
| | - Anna Duszyk-Bogorodzka
- Behavioural Neuroscience Lab, Institute of Psychology, SWPS University, 03-815 Warsaw, Poland;
| | - Piotr Biegański
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (M.D.); (P.B.)
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22
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Muthu C, Resmi AN, Ajayakumar A, Ravindran NEA, Dayal G, Jinesh KB, Szaciłowski K, Vijayakumar C. Self-Assembly of Delta-Formamidinium Lead Iodide Nanoparticles to Nanorods: Study of Memristor Properties and Resistive Switching Mechanism. Small 2024:e2304787. [PMID: 38243886 DOI: 10.1002/smll.202304787] [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: 06/07/2023] [Revised: 12/02/2023] [Indexed: 01/22/2024]
Abstract
In the quest for advanced memristor technologies, this study introduces the synthesis of delta-formamidinium lead iodide (δ-FAPbI3 ) nanoparticles (NPs) and their self-assembly into nanorods (NRs). The formation of these NRs is facilitated by iodide vacancies, promoting the fusion of individual NPs at higher concentrations. Notably, these NRs exhibit robust stability under ambient conditions, a distinctive advantage attributed to the presence of capping ligands and a crystal lattice structured around face-sharing octahedra. When employed as the active layer in resistive random-access memory devices, these NRs demonstrate exceptional bipolar switching properties. A remarkable on/off ratio (105 ) is achieved, surpassing the performances of previously reported low-dimensional perovskite derivatives and α-FAPbI3 NP-based devices. This enhanced performance is attributed to the low off-state current owing to the reduced number of halide vacancies, intrinsic low dimensionality, and the parallel alignment of NRs on the FTO substrate. This study not only provides significant insights into the development of superior materials for memristor applications but also opens new avenues for exploring low-dimensional perovskite derivatives in advanced electronic devices.
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Affiliation(s)
- Chinnadurai Muthu
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695 019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - A N Resmi
- Department of Physics, Indian Institute of Space Science and Technology (IIST), Thiruvananthapuram, 695 547, India
| | - Avija Ajayakumar
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695 019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - N E Aswathi Ravindran
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695 019, India
| | - G Dayal
- Department of Physics, Indian Institute of Space Science and Technology (IIST), Thiruvananthapuram, 695 547, India
| | - K B Jinesh
- Department of Physics, Indian Institute of Space Science and Technology (IIST), Thiruvananthapuram, 695 547, India
| | - Konrad Szaciłowski
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, Krakow, 30 059, Poland
| | - Chakkooth Vijayakumar
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695 019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
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23
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Łabuz J, Banaś AK, Zgłobicki P, Bażant A, Sztatelman O, Giza A, Lasok H, Prochwicz A, Kozłowska-Mroczek A, Jankowska U, Hermanowicz P. Phototropin2 3'UTR overlaps with the AT5G58150 gene encoding an inactive RLK kinase. BMC Plant Biol 2024; 24:55. [PMID: 38238701 PMCID: PMC10795372 DOI: 10.1186/s12870-024-04732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND This study examines the biological implications of an overlap between two sequences in the Arabidopsis genome, the 3'UTR of the PHOT2 gene and a putative AT5G58150 gene, encoded on the complementary strand. AT5G58150 is a probably inactive protein kinase that belongs to the transmembrane, leucine-rich repeat receptor-like kinase family. Phot2 is a membrane-bound UV/blue light photoreceptor kinase. Thus, both proteins share their cellular localization, on top of the proximity of their loci. RESULTS The extent of the overlap between 3'UTR regions of AT5G58150 and PHOT2 was found to be 66 bp, using RACE PCR. Both the at5g58150 T-DNA SALK_093781C (with insertion in the promoter region) and 35S::AT5G58150-GFP lines overexpress the AT5G58150 gene. A detailed analysis did not reveal any substantial impact of PHOT2 or AT5G58150 on their mutual expression levels in different light and osmotic stress conditions. AT5G58150 is a plasma membrane protein, with no apparent kinase activity, as tested on several potential substrates. It appears not to form homodimers and it does not interact with PHOT2. Lines that overexpress AT5G58150 exhibit a greater reduction in lateral root density due to salt and osmotic stress than wild-type plants, which suggests that AT5G58150 may participate in root elongation and formation of lateral roots. In line with this, mass spectrometry analysis identified proteins with ATPase activity, which are involved in proton transport and cell elongation, as putative interactors of AT5G58150. Membrane kinases, including other members of the LRR RLK family and BSK kinases (positive regulators of brassinosteroid signalling), can also act as partners for AT5G58150. CONCLUSIONS AT5G58150 is a membrane protein that does not exhibit measurable kinase activity, but is involved in signalling through interactions with other proteins. Based on the interactome and root architecture analysis, AT5G58150 may be involved in plant response to salt and osmotic stress and the formation of roots in Arabidopsis.
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Affiliation(s)
- Justyna Łabuz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland.
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Giza
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Hanna Lasok
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Aneta Prochwicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Anna Kozłowska-Mroczek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Paweł Hermanowicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
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24
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Jaśkiewicz M, Neubauer D, Sikora K, Bauer M, Bartoszewska S, Błażewicz I, Marek D, Barańska-Rybak W, Kamysz W. The Study of Antistaphylococcal Potential of Omiganan and Retro-Omiganan Under Flow Conditions. Probiotics Antimicrob Proteins 2024:10.1007/s12602-023-10197-w. [PMID: 38224448 DOI: 10.1007/s12602-023-10197-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/16/2024]
Abstract
Staphylococcus aureus is considered one of the leading pathogens responsible for infections in humans and animals. The heterogeneous nature of diseases caused by these bacteria is due to the occurrence of multiple strains, differentiated by several mechanisms of antibiotic resistance and virulence factors. One of these is the ability to form biofilm. Biofilm-associated bacteria exhibit a different phenotype that protects them from external factors such as the activity of immune system or antimicrobial substances. Moreover, it has been shown that the majority of persistent and recurrent infections are associated with the presence of the biofilm. Omiganan, an analog of indolicidin - antimicrobial peptide (AMP) derived from bovine neutrophil granules, was found to exhibit high antistaphylococcal and antibiofilm potential. Furthermore, its analog with a reversed sequence (retro-omiganan) was found to display enhanced activity against a variety of pathogens. Based on experience of our group, we found out that counterion exchange can improve the antistaphylococcal activity of AMPs. The aim of this study was to investigate the activity of both compounds against S. aureus biofilm under flow conditions. The advantage of this approach was that it offered the opportunity to form and characterize the biofilm under more controlled conditions. To do this, unique flow cells made of polydimethylsiloxane (PDMS) were developed. The activity against pre-formed biofilm as well as AMPs-treated bacteria was measured. Also, the incorporation of omiganan and retro-omiganan into the channels was conducted to learn whether or not it would inhibit the development of biofilm. The results of the microbiological tests ultimately confirmed the high potential of the omiganan and its retro-analog as well as the importance of counterion exchange in terms of antimicrobial examination. We found out that retro-omiganan trifluoroacetate had the highest biofilm inhibitory properties, however, acetates of both compounds exhibited the highest activity against planktonic and biofilm cultures. Moreover, the developed methodology of investigation under flow conditions allows the implementation of the studies under flow conditions to other compounds.
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Affiliation(s)
- Maciej Jaśkiewicz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
- International Research Agenda 3P-Medicine Laboratory, Medical University of Gdańsk, Building No. 5, Dębinki 7, 80-211, Gdańsk, Poland.
| | - Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Karol Sikora
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Marta Bauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Izabela Błażewicz
- Department of Dermatology, Venereology and Allergology, Medical University of Gdańsk, Mariana Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Dariusz Marek
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Wioletta Barańska-Rybak
- Department of Dermatology, Venereology and Allergology, Medical University of Gdańsk, Mariana Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
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25
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Golec de Zavala A, Förster C, Ziegler M, Nalberczak-Skóra M, Ciesielski P, Mazurkiewicz M. The shape of the change: Cumulative and incremental changes in daily mood during mobile-app-supported mindfulness training. Appl Psychol Health Well Being 2024. [PMID: 38183357 DOI: 10.1111/aphw.12518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/01/2023] [Indexed: 01/08/2024]
Abstract
Understanding of the exact trajectories of mood improvements during mindfulness practice helps to optimize mindfulness-based interventions. The Mindfulness-to-Meaning model expects mood improvements to be linear, incremental, and cumulative. Our findings align with this expectation. We used multilevel growth curve models to analyze daily changes in positive mood reported by 190 Polish participants during 42 days of a mobile-app-supported, mindfulness-based intervention. The daily positive mood increased among 83.68% of participants. Participants who started the training reported worse mood improved more and faster than participants with better mood at the baseline. Dispositional mindfulness and narcissism - individual difference variables associated with high vs. low emotion regulation ability, respectively - were not associated with mood improvement trajectories. A small group of participants (16.32%) showed a steady decline in positive mood during the intervention. The results underscore the importance of a more comprehensive understanding of individual variability in benefiting from mindfulness-based interventions.
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Affiliation(s)
| | - Chiara Förster
- Psychological Institute, Humboldt University, Berlin, Germany
| | | | | | - Pawel Ciesielski
- Faculty of Psychology and Cognitive Science, Adam Mickiewicz University, Poznań, Poland
| | - Magdalena Mazurkiewicz
- Department of Psychology, SWPS University of Social Sciences and Humanities, Warsaw, Poland
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26
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Hiller KP, Winkelmann A, Hourahine B, Starosta B, Alasmari A, Feng P, Wang T, Parbrook PJ, Zubialevich VZ, Hagedorn S, Walde S, Weyers M, Coulon PM, Shields PA, Bruckbauer J, Trager-Cowan C. Imaging Threading Dislocations and Surface Steps in Nitride Thin Films Using Electron Backscatter Diffraction. Microsc Microanal 2023; 29:1879-1888. [PMID: 37947075 DOI: 10.1093/micmic/ozad118] [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: 05/23/2023] [Revised: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
Extended defects, like threading dislocations, are detrimental to the performance of optoelectronic devices. In the scanning electron microscope, dislocations are traditionally imaged using diodes to monitor changes in backscattered electron intensity as the electron beam is scanned over the sample, with the sample positioned so the electron beam is at, or close to the Bragg angle for a crystal plane/planes. Here, we use a pixelated detector instead of single diodes, specifically an electron backscatter diffraction (EBSD) detector. We present postprocessing techniques to extract images of dislocations and surface steps, for a nitride thin film, from measurements of backscattered electron intensities and intensity distributions in unprocessed EBSD patterns. In virtual diode (VD) imaging, the backscattered electron intensity is monitored for a selected segment of the unprocessed EBSD patterns. In center of mass (COM) imaging, the position of the center of the backscattered electron intensity distribution is monitored. Additionally, both methods can be combined (VDCOM). Using both VD and VDCOM, images of only threading dislocations, or dislocations and surface steps can be produced, with VDCOM images exhibiting better signal-to-noise. The applicability of VDCOM imaging is demonstrated across a range of nitride semiconductor thin films, with varying surface step and dislocation densities.
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Affiliation(s)
- Kieran P Hiller
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
| | - Aimo Winkelmann
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Kraków 30-055, Poland
| | - Ben Hourahine
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
| | - Bohdan Starosta
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
| | - Aeshah Alasmari
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
| | - Peng Feng
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Tao Wang
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Peter J Parbrook
- Tyndall National Institute, University College Cork, Cork T12 R5CP, Ireland
| | | | - Sylvia Hagedorn
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, D-12489 Berlin, Germany
| | - Sebastian Walde
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, D-12489 Berlin, Germany
| | - Markus Weyers
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, D-12489 Berlin, Germany
| | - Pierre-Marie Coulon
- Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK
- CNRS-CRHEA, Université Côte d'Azur, 06560 Valbonne, France
| | - Philip A Shields
- Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK
| | - Jochen Bruckbauer
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
| | - Carol Trager-Cowan
- Advanced Materials Diffraction Lab, Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK
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Pilowsky JA, Brown SC, Llamas B, van Loenen AL, Kowalczyk R, Hofman-Kamińska E, Manaseryan NH, Rusu V, Križnar M, Rahbek C, Fordham DA. Millennial processes of population decline, range contraction and near extinction of the European bison. Proc Biol Sci 2023; 290:20231095. [PMID: 38087919 PMCID: PMC10716654 DOI: 10.1098/rspb.2023.1095] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.
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Affiliation(s)
- July A. Pilowsky
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Stuart C. Brown
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen K 1350, Denmark
| | - Bastien Llamas
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, South Australia 5005, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, South Australia 5001, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ayla L. van Loenen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | | | - Ninna H. Manaseryan
- The Scientific Centre of Zoology and Hydroecology of National Academy of Sciences of Armenia, Institute of Zoology, 0014 Yerevan, Republic of Armenia
| | - Viorelia Rusu
- Institute of Zoology, Academy of Sciences of Moldova, Chisinau MD-2028, Republic of Moldova
| | - Matija Križnar
- Slovenian Museum of Natural History, Department of Geology, SI-1001 Ljubljana, Slovenia
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M 5230, Denmark
- Institute of Ecology, Peking University, Beijing, People's Republic of China
| | - Damien A. Fordham
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
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28
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Doser M, Farrar G, Kornakov G. Searching for a dark matter particle with anti-protonic atoms. Eur Phys J C Part Fields 2023; 83:1149. [PMID: 38125559 PMCID: PMC10728242 DOI: 10.1140/epjc/s10052-023-12319-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
A wide range of dark matter candidates have been proposed and are actively being searched for in a large number of experiments, both at high (TeV) and low (sub meV) energies. One dark matter candidate, a deeply bound uuddss sexaquark, S , with mass ∼ 2 GeV (having the same quark content as the hypothesized H-dibaryon, but long lived) is particularly difficult to explore experimentally. In this paper, we propose a scheme in which such a state could be produced at rest through the formation of p ¯ -3 He antiprotonic atoms and their annihilation into S + K + K + π - , identified both through the unique tag of a S = + 2 , Q = + 1 final state, as well as through full kinematic reconstruction of the final state recoiling against it.
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Affiliation(s)
- Michael Doser
- CERN, Esplanade des Particules 1, 1211 Geneva, Switzerland
| | - Glennys Farrar
- Center for Cosmology and Particle Physics, New York University, New York, NY 10003 USA
| | - Georgy Kornakov
- Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warsaw, Poland
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29
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Karbowski J, Urban P. Information encoded in volumes and areas of dendritic spines is nearly maximal across mammalian brains. Sci Rep 2023; 13:22207. [PMID: 38097675 PMCID: PMC10721930 DOI: 10.1038/s41598-023-49321-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
Many experiments suggest that long-term information associated with neuronal memory resides collectively in dendritic spines. However, spines can have a limited size due to metabolic and neuroanatomical constraints, which should effectively limit the amount of encoded information in excitatory synapses. This study investigates how much information can be stored in the population of sizes of dendritic spines, and whether it is optimal in any sense. It is shown here, using empirical data for several mammalian brains across different regions and physiological conditions, that dendritic spines nearly maximize entropy contained in their volumes and surface areas for a given mean size in cortical and hippocampal regions. Although both short- and heavy-tailed fitting distributions approach [Formula: see text] of maximal entropy in the majority of cases, the best maximization is obtained primarily for short-tailed gamma distribution. We find that most empirical ratios of standard deviation to mean for spine volumes and areas are in the range [Formula: see text], which is close to the theoretical optimal ratios coming from entropy maximization for gamma and lognormal distributions. On average, the highest entropy is contained in spine length ([Formula: see text] bits per spine), and the lowest in spine volume and area ([Formula: see text] bits), although the latter two are closer to optimality. In contrast, we find that entropy density (entropy per spine size) is always suboptimal. Our results suggest that spine sizes are almost as random as possible given the constraint on their size, and moreover the general principle of entropy maximization is applicable and potentially useful to information and memory storing in the population of cortical and hippocampal excitatory synapses, and to predicting their morphological properties.
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Affiliation(s)
- Jan Karbowski
- Institute of Applied Mathematics and Mechanics, University of Warsaw, Warsaw, Poland.
| | - Paulina Urban
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Laboratory of Databases and Business Analytics, National Information Processing Institute, National Research Institute, Warsaw, Poland
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30
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Lenda M, Steudel B, Skórka P, Zagrodzka ZB, Moroń D, Bączek-Kwinta R, Janowiak F, Baran A, Possingham HP, Knops JMH. Multiple invasive species affect germination, growth, and photosynthesis of native weeds and crops in experiments. Sci Rep 2023; 13:22146. [PMID: 38092817 PMCID: PMC10719303 DOI: 10.1038/s41598-023-48421-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Alien plant species regularly and simultaneously invade agricultural landscapes and ecosystems; however, the effects of co-invasion on crop production and native biodiversity have rarely been studied. Secondary metabolites produced by alien plants may be allelopathic; if they enter the soil, they may be transported by agricultural activities, negatively affecting crop yield and biodiversity. It is unknown whether substances from different alien species in combination have a greater impact on crops and wild plants than if they are from only one of the alien species. In this study, we used a set of common garden experiments to test the hypothesis that mixed extracts from two common invasive species have synergistic effects on crops and weeds (defined as all non-crop plants) in European agricultural fields compared to single-species extracts. We found that both the combined and individual extracts had detrimental effects on the seed germination, seedling growth, biomass, and photosynthetic performance of both crops and weeds. We found that the negative effect of mixed extracts was not additive and that crop plants were more strongly affected by invasive species extracts than the weeds. Our results are important for managing invasive species in unique ecosystems on agricultural land and preventing economic losses in yield production.
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Affiliation(s)
- Magdalena Lenda
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland
| | - Bastian Steudel
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China.
| | - Piotr Skórka
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland
| | | | - Dawid Moroń
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Renata Bączek-Kwinta
- Department of Plant Breeding, Physiology, and Seed Science, Faculty of Agriculture and Economics, University of Agriculture in Cracow, Podłużna 3, 30-239, Kraków, Poland
| | - Franciszek Janowiak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Agnieszka Baran
- Department of Agricultural and Environmental Chemistry, Faculty of Agriculture and Economics, University of Agriculture in Cracow, Al. Mickiewicza 21, 31-120, Kraków, Poland
| | - Hugh P Possingham
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Johannes M H Knops
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China
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Radziemska M, Gusiatin MZ, Cydzik-Kwiatkowska A, Blazejczyk A, Majewski G, Jaskulska I, Brtnicky M. Effect of freeze-thaw manipulation on phytostabilization of industrially contaminated soil with halloysite nanotubes. Sci Rep 2023; 13:22175. [PMID: 38092858 PMCID: PMC10719333 DOI: 10.1038/s41598-023-49698-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
The latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing-thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing-thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT's role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC's negative effect on microbial diversity and increased Planctomycetia abundance.
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Affiliation(s)
- Maja Radziemska
- Institute of Environmental Engineering, Warsaw University of Life Sciences, 02-776, Warsaw, Poland.
| | - Mariusz Z Gusiatin
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | | | - Aurelia Blazejczyk
- Institute of Civil Engineering, Warsaw University of Life Sciences, 02-776, Warsaw, Poland
| | - Grzegorz Majewski
- Institute of Environmental Engineering, Warsaw University of Life Sciences, 02-776, Warsaw, Poland
| | - Iwona Jaskulska
- Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Martin Brtnicky
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Mendel University in Brno, 613 00, Brno, Czech Republic
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32
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Vargas-Castro I, Crespo-Picazo JL, Fayos M, Jiménez-Martínez MDLÁ, Torre-Fuentes L, Álvarez J, Moura AE, Hernández M, Buendía A, Barroso-Arévalo S, García-Seco T, Pérez-Sancho M, De Miguel MJ, Andrés-Barranco S, Marco-Cabedo V, Peñin-Villahoz G, Muñoz PM, Domínguez L, García-Párraga D, Sánchez-Vizcaíno JM. New insights into the pathogenesis and transmission of Brucella pinnipedialis: systemic infection in two bottlenose dolphins ( Tursiops truncatus). Microbiol Spectr 2023; 11:e0199723. [PMID: 37800951 PMCID: PMC10848334 DOI: 10.1128/spectrum.01997-23] [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: 05/12/2023] [Accepted: 08/08/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Brucella spp. are zoonotic pathogens that can affect both terrestrial and marine mammals. Brucella ceti has been identified in various cetacean species, but only one sequence type (ST27) has been reported in humans. However, it is important to conduct surveillance studies to better understand the impact of marine Brucella species on marine mammals, a typically understudied host group. Here, we describe a systemic infection by two related strains of Brucella pinnipedialis (ST25) in a couple of live-stranded bottlenose dolphins, with more severe lesions in the younger animal. Furthermore, B. pinnipedialis was first detected in milk from a female cetacean that stranded with its offspring. Our study reveals novel insights into the epidemiology and pathological consequences of B. pinnipedialis infections in cetaceans, emphasizing the crucial importance of ongoing surveillance and accurate diagnosis to understand the impact of this pathogen on marine mammal populations.
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Affiliation(s)
- Ignacio Vargas-Castro
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | | | - Manena Fayos
- Centro de Recuperación de Fauna Silvestre de Cantabria, Santander, Spain
| | | | - Laura Torre-Fuentes
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - André E. Moura
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Hernández
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | - Aranzazu Buendía
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Sandra Barroso-Arévalo
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Teresa García-Seco
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - María Jesús De Miguel
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA) - Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, España, Spain
| | - Sara Andrés-Barranco
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA) - Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, España, Spain
| | - Vicente Marco-Cabedo
- />Fundación Oceanogràfic. Oceanogràfic. Ciudad de las Artes y las Ciencias, Valencia, Spain
| | | | - Pilar María Muñoz
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA) - Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, España, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Daniel García-Párraga
- />Fundación Oceanogràfic. Oceanogràfic. Ciudad de las Artes y las Ciencias, Valencia, Spain
| | - José Manuel Sánchez-Vizcaíno
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
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33
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Jurasz K, Kościelnik D, Szyduczyński J, Machowski W. A New Successive Time Balancing Time-to-Digital Conversion Method. Sensors (Basel) 2023; 23:9712. [PMID: 38139557 PMCID: PMC10747889 DOI: 10.3390/s23249712] [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: 09/20/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
This paper presents a new self-clocked time-to-digital conversion method based on a binary successive approximation (SA) algorithm. Its novelty consists in combining fully clockless operation with direct conversion of the measured time interval. The lack of any reference clock makes the presented method potentially predisposed to low-power solutions. Furthermore, its circuit representation is extremely simple, thereby the ability to direct conversion of time intervals is not burdened by a significant amount of components. The method is intended to measure relatively long time intervals, i.e., hundreds of microseconds. Therefore, it is suitable for e.g., biomedical applications using time-mode signal processing.
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Affiliation(s)
- Konrad Jurasz
- Department of Electronics, AGH University of Science and Technology, 30-059 Krakow, Poland; (J.S.); (W.M.)
| | - Dariusz Kościelnik
- Department of Electronics, AGH University of Science and Technology, 30-059 Krakow, Poland; (J.S.); (W.M.)
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34
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Want A, Staniak K, Grabowska-Pyrzewicz W, Fesiuk A, Barczak A, Gabryelewicz T, Kulczyńska-Przybik A, Mroczko B, Wojda U. Optimized RT-qPCR and a novel normalization method for validating circulating miRNA biomarkers in ageing-related diseases. Sci Rep 2023; 13:20869. [PMID: 38012217 PMCID: PMC10682428 DOI: 10.1038/s41598-023-47971-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Circulating miRNAs have potential as minimally invasive biomarkers for diagnosing various diseases, including ageing-related disorders such as Alzheimer's disease (AD). However, the lack of standardization in the common analysis method, RT-qPCR, and specifically in the normalization step, has resulted in inconsistent data across studies, hindering miRNA clinical implementation as well as basic research. To address this issue, this study proposes an optimized protocol for key steps in miRNA profiling, which incorporates absorbance-based haemolysis detection for assessing sample quality, double spike-in controls for miRNA isolation and reverse transcription, and the use of 7 stable normalizers verified in an aging population, including healthy subjects and individuals at different stages of Alzheimer's disease (140 subjects). The stability of these 7 normalizers was demonstrated using our novel method called BestmiRNorm for identifying optimal normalizers. BestmiRNorm, developed utilizing the Python programming language, enables the assessment of up to 11 potential normalizers. The standardized application of this optimized RT-qPCR protocol and the recommended normalizers are crucial for the development of miRNAs as biomarkers for AD and other ageing-related diseases in clinical diagnostics and basic research.
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Affiliation(s)
- Andrew Want
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Staniak
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wioleta Grabowska-Pyrzewicz
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Fesiuk
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Dementia Diseases Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Gabryelewicz
- Dementia Diseases Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kulczyńska-Przybik
- Department of Neurodegeneration Diagnostics, Faculty of Medicine, Medical University of Bialystok, Białystok, Poland
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Faculty of Medicine, Medical University of Bialystok, Białystok, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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35
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Miklaszewska M, Zienkiewicz K, Klugier-Borowska E, Rygielski M, Feussner I, Zienkiewicz A. CALEOSIN 1 interaction with AUTOPHAGY-RELATED PROTEIN 8 facilitates lipid droplet microautophagy in seedlings. Plant Physiol 2023; 193:2361-2380. [PMID: 37619984 PMCID: PMC10663143 DOI: 10.1093/plphys/kiad471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/16/2023] [Accepted: 08/05/2023] [Indexed: 08/26/2023]
Abstract
Lipid droplets (LDs) of seed tissues are storage organelles for triacylglycerols (TAGs) that provide the energy and carbon for seedling establishment. In the major route of LD degradation (lipolysis), TAGs are mobilized by lipases. However, LDs may also be degraded via lipophagy, a type of selective autophagy, which mediates LD delivery to vacuoles or lysosomes. The exact mechanisms of LD degradation and the mobilization of their content in plants remain unresolved. Here, we provide evidence that LDs are degraded via a process morphologically resembling microlipophagy in Arabidopsis (Arabidopsis thaliana) seedlings. We observed the entry and presence of LDs in the central vacuole as well as their breakdown. Moreover, we show co-localization of AUTOPHAGY-RELATED PROTEIN 8b (ATG8b) and LDs during seed germination and localization of lipidated ATG8 (ATG8-PE) to the LD fraction. We further demonstrate that structural LD proteins from the caleosin family, CALEOSIN 1 (CLO1), CALEOSIN 2 (CLO2), and CALEOSIN 3 (CLO3), interact with ATG8 proteins and possess putative ATG8-interacting motifs (AIMs). Deletion of the AIM localized directly before the proline knot disrupts the interaction of CLO1 with ATG8b, suggesting a possible role of this region in the interaction between these proteins. Collectively, we provide insights into LD degradation by microlipophagy in germinating seeds with a particular focus on the role of structural LD proteins in this process.
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Affiliation(s)
- Magdalena Miklaszewska
- Department of Plant Physiology and Biotechnology, University of Gdańsk, Wita Stwosza 59, Gdańsk 80-308, Poland
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
| | - Krzysztof Zienkiewicz
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Ewa Klugier-Borowska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Marcin Rygielski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Ivo Feussner
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
| | - Agnieszka Zienkiewicz
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
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36
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Shaterian Z, Horestani AK, Martín F, Mrozowski M. Design of novel highly sensitive sensors for crack detection in metal surfaces: theoretical foundation and experimental validation. Sci Rep 2023; 13:18540. [PMID: 37899369 PMCID: PMC10613631 DOI: 10.1038/s41598-023-45556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023] Open
Abstract
The application of different types of microwave resonators for sensing cracks in metallic structures has been subject of many studies. While most studies have been focused on improving the sensitivity of planar crack sensors, the theoretical foundation of the topic has not been treated in much detail. The major objective of this study is to perform an exhaustive study of the principles and theoretical foundations for crack sensing based on planar microwave resonators, especially defective ground structures (DGS) including complementary split ring resonators (CSRRs). The analysis is carried out from the equivalent circuit model as well as the electromagnetic (EM) field perspectives, and guidelines for the design of crack sensors with high sensitivity are developed. Numerical and experimental validation of the provided theoretical analysis is another aim of this article. With this aim, the developed guidelines are used to design a crack sensor based on a single-ring CSRR. It is shown that the sensitivity of the proposed sensor is almost three times higher than the sensitivity of a conventional double-ring CSRR. Moreover, it is demonstrated that folded dumbbell-shape DGS resonators can be used to achieve even higher sensitivities. The CSRR-based crack sensors presented in this study and other studies available in the literature are only sensitive to cracks with a specific orientation. To address this limitation, a modified version of the DGS is proposed to sense cracks with arbitrary orientations at the cost of lower sensitivity. The performance of all the presented sensors is validated through EM simulation, equivalent circuit model extraction, and measurement of the fabricated prototypes.
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Affiliation(s)
- Zahra Shaterian
- Department of Electrical Engineering, Technical and Vocational University (TVU), 14357-61137, Tehran, Iran.
- Department of Microwave and Antenna Engineering, Faculty of Electronics, Telecommunications, and Informatics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Ali K Horestani
- Department of Microwave and Antenna Engineering, Faculty of Electronics, Telecommunications, and Informatics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
- Wireless Telecommunication Group, Khayyam Research Institute, Ministry of Science, Research and Technology, Tehran, 64891, Iran.
| | - Ferran Martín
- CIMITEC, Departament d'Enginyeria Electrònica, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Michal Mrozowski
- Department of Microwave and Antenna Engineering, Faculty of Electronics, Telecommunications, and Informatics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
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37
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Wegrzyn K, Oliwa M, Nowacka M, Zabrocka E, Bury K, Purzycki P, Czaplewska P, Pipka J, Giraldo R, Konieczny I. Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation. Nucleic Acids Res 2023; 51:10551-10567. [PMID: 37713613 PMCID: PMC10602881 DOI: 10.1093/nar/gkad740] [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: 02/23/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
For DNA replication initiation in Bacteria, replication initiation proteins bind to double-stranded DNA (dsDNA) and interact with single-stranded DNA (ssDNA) at the replication origin. The structural-functional relationship of the nucleoprotein complex involving initiator proteins is still elusive and different models are proposed. In this work, based on crosslinking combined with mass spectrometry (MS), the analysis of mutant proteins and crystal structures, we defined amino acid residues essential for the interaction between plasmid Rep proteins, TrfA and RepE, and ssDNA. This interaction and Rep binding to dsDNA could not be provided in trans, and both are important for dsDNA melting at DNA unwinding element (DUE). We solved two crystal structures of RepE: one in a complex with ssDNA DUE, and another with both ssDNA DUE and dsDNA containing RepE-specific binding sites (iterons). The amino acid residues involved in interaction with ssDNA are located in the WH1 domain in stand β1, helices α1 and α2 and in the WH2 domain in loops preceding strands β1' and β2' and in these strands. It is on the opposite side compared to RepE dsDNA-recognition interface. Our data provide evidence for a loop-back mechanism through which the plasmid replication initiator molecule accommodates together dsDNA and ssDNA.
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Affiliation(s)
- Katarzyna Wegrzyn
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Monika Oliwa
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Marzena Nowacka
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Elżbieta Zabrocka
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Katarzyna Bury
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Piotr Purzycki
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Justyna Pipka
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Rafael Giraldo
- Centro de Investigaciones Biológicas – CSIC, E28040 Madrid, Spain
| | - Igor Konieczny
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
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38
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Pustelny K, Grygier P, Barzowska A, Pucelik B, Matsuda A, Mrowiec K, Slugocka E, Popowicz GM, Dubin G, Czarna A. Binding mechanism and biological effects of flavone DYRK1A inhibitors for the design of new antidiabetics. Sci Rep 2023; 13:18114. [PMID: 37872245 PMCID: PMC10593742 DOI: 10.1038/s41598-023-44810-3] [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: 06/06/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The selective inhibition of kinases from the diabetic kinome is known to promote the regeneration of beta cells and provide an opportunity for the curative treatment of diabetes. The effect can be achieved by carefully tailoring the selectivity of inhibitor toward a particular kinase, especially DYRK1A, previously associated with Down syndrome and Alzheimer's disease. Recently DYRK1A inhibition has been shown to promote both insulin secretion and beta cells proliferation. Here, we show that commonly available flavones are effective inhibitors of DYRK1A. The observed biochemical activity of flavone compounds is confirmed by crystal structures solved at 2.06 Å and 2.32 Å resolution, deciphering the way inhibitors bind in the ATP-binding pocket of the kinase, which is driven by the arrangement of hydroxyl moieties. We also demonstrate antidiabetic properties of these biomolecules and prove that they could be further improved by therapy combined with TGF-β inhibitors. Our data will allow future structure-based optimization of the presented scaffolds toward potent, bioavailable and selective anti-diabetic drugs.
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Affiliation(s)
- Katarzyna Pustelny
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Przemyslaw Grygier
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Agata Barzowska
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Barbara Pucelik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Alex Matsuda
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Krzysztof Mrowiec
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Emilia Slugocka
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Anna Czarna
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland.
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Mertowska P, Mertowski S, Smolak K, Pasiarski M, Smok-Kalwat J, Góźdź S, Grywalska E. Exploring the Significance of Immune Checkpoints and EBV Reactivation in Antibody Deficiencies with Near-Normal Immunoglobulin Levels or Hyperimmunoglobulinemia. Cancers (Basel) 2023; 15:5059. [PMID: 37894426 PMCID: PMC10605741 DOI: 10.3390/cancers15205059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
This study delves into the intricate landscape of primary immunodeficiencies, with a particular focus on antibody deficiencies characterized by near-normal immunoglobulin levels or hyperimmunoglobulinemia. Contrary to the conventional focus on genetic dysregulation, these studies investigate the key roles of immune checkpoints, such as PD-1/PD-L1, CTLA-4/CD86, and CD200R/CD200, on selected subpopulations of T and B lymphocytes and their serum concentrations of soluble forms in patients recruited for the studies in healthy volunteers. In addition, the studies also show the role of Epstein-Barr virus (EBV) reactivation and interactions with tested pathways of immune checkpoints involved in the immunopathogenesis of this disease. By examining the context of antibody deficiencies, this study sheds light on the nuanced interplay of factors beyond genetics, particularly the immune dysregulations that occur in the course of this type of disease and the potential role of EBV reactivation, which affects the clinical presentation of patients and may contribute to the development of cancer in the future, especially related to hematological malignancies.
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Affiliation(s)
- Paulina Mertowska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (P.M.); (E.G.)
| | - Sebastian Mertowski
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (P.M.); (E.G.)
| | - Konrad Smolak
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (P.M.); (E.G.)
| | - Marcin Pasiarski
- Department of Immunology, Faculty of Health Sciences, Jan Kochanowski University, 25-317 Kielce, Poland;
- Department of Hematology, Holy Cross Cancer Centre, 25-734 Kielce, Poland; (J.S.-K.); (S.G.)
| | - Jolanta Smok-Kalwat
- Department of Hematology, Holy Cross Cancer Centre, 25-734 Kielce, Poland; (J.S.-K.); (S.G.)
| | - Stanisław Góźdź
- Department of Hematology, Holy Cross Cancer Centre, 25-734 Kielce, Poland; (J.S.-K.); (S.G.)
- Institute of Medical Science, Collegium Medicum, Jan Kochanowski University of Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland
| | - Ewelina Grywalska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (P.M.); (E.G.)
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40
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Chumak V, Zhydachevskyy Y, Voloskyi V, Bakhanova E, Stasiv V, Gieszczyk W, Ubizskii S, Berkowski M, Suchocki A. Experimental validation of energy dependences of YALO3:Mn TL detectors: irradiation to ISO radiation qualities. Radiat Prot Dosimetry 2023; 199:1696-1699. [PMID: 37819308 DOI: 10.1093/rpd/ncad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/26/2023] [Accepted: 03/01/2023] [Indexed: 10/13/2023]
Abstract
The effect of application of filters, made of different materials and various thickness, is studied by Monte Carlo calculations using MCNP6.2 code. The calculated data were validated by experimental studies (benchmark tests). Experimental results obtained for YAlO3:Mn high-Z TL detectors irradiated to different standard ISO radiation qualities (X-ray series N-40, N-60, N-80, N-100, N-120, N-150 and N-200 as well as isotopic series S-Cs) modified by various metal (copper and aluminum) filters of thickness of 0.5, 0.8 and 1 mm. The experimental results are compared with results of Monte Carlo simulations done for the same 'radiation-attenuator-detector' combinations and geometry. Obtained results show good consistence between the experimental and calculated data that testifies adequacy of the used calculations and their applicability to modeling of modification of an output from the high-Z detectors exposed to photons of various energies.
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Affiliation(s)
- Vadim Chumak
- National Research Centre for Radiation Medicine NAMS Ukraine, 04050, Yu.Illyenko 53 Kyiv, Ukraine
- RPE DOSIMETRICA, Kyiv, Ukraine, 04119, P.O. box 40, Kyiv, Ukraine
| | - Yaroslav Zhydachevskyy
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland
| | - Vitaliy Voloskyi
- National Research Centre for Radiation Medicine NAMS Ukraine, 04050, Yu.Illyenko 53 Kyiv, Ukraine
- RPE DOSIMETRICA, Kyiv, Ukraine, 04119, P.O. box 40, Kyiv, Ukraine
| | - Elena Bakhanova
- National Research Centre for Radiation Medicine NAMS Ukraine, 04050, Yu.Illyenko 53 Kyiv, Ukraine
- RPE DOSIMETRICA, Kyiv, Ukraine, 04119, P.O. box 40, Kyiv, Ukraine
| | - Vasyl Stasiv
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland
| | - Wojciech Gieszczyk
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, Kraków 31-242, Poland
| | - Sergii Ubizskii
- Lviv Polytechnic National University, S. Bandera 12, Lviv 79013, Ukraine
| | - Marek Berkowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland
| | - Andrzej Suchocki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland
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41
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Kaushal V, Klim J, Skoneczna A, Kurlandzka A, Enkhbaatar T, Kaczanowski S, Zielenkiewicz U. Apoptotic Factors Are Evolutionarily Conserved Since Mitochondrial Domestication. Genome Biol Evol 2023; 15:evad154. [PMID: 37616576 PMCID: PMC10565124 DOI: 10.1093/gbe/evad154] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/18/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
The mechanisms initiating apoptotic programmed cell death in diverse eukaryotes are very similar. Basically, the mitochondrial permeability transition activates apoptotic proteases, DNases, and flavoproteins such as apoptosis-inducing factors (AIFs). According to the hypothesis of the endosymbiotic origin of apoptosis, these mechanisms evolved during mitochondrial domestication. Various phylogenetic analyses, including ours, have suggested that apoptotic factors were eubacterial protomitochondrial toxins used for killing protoeukaryotic hosts. Here, we tested whether the function of yeast Saccharomyces cerevisiae apoptotic proteases (metacaspases Mca1 and Nma111), DNase Nuc1, and flavoprotein Ndi1 can be substituted with orthologs from remotely related eukaryotes such as plants, protists, and eubacteria. We found that orthologs of remotely related eukaryotic and even eubacterial proteins can initiate apoptosis in yeast when triggered by chemical stresses. This observation suggests that apoptotic mechanisms have been maintained since mitochondrial domestication, which occurred approximately 1,800 Mya. Additionally, it supports the hypothesis that some of these apoptotic factors could be modified eubacterial toxins.
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Affiliation(s)
- Vandana Kaushal
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Joanna Klim
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Szymon Kaczanowski
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
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42
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Zheng T, Runowski M, Martín IR, Soler-Carracedo K, Peng L, Skwierczyńska M, Sójka M, Barzowska J, Mahlik S, Hemmerich H, Rivera-López F, Kulpiński P, Lavín V, Alonso D, Peng D. Mechanoluminescence and Photoluminescence Heterojunction for Superior Multimode Sensing Platform of Friction, Force, Pressure, and Temperature in Fibers and 3D-Printed Polymers. Adv Mater 2023; 35:e2304140. [PMID: 37399662 DOI: 10.1002/adma.202304140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
Endowing a single material with various types of luminescence, that is, exhibiting a simultaneous optical response to different stimuli, is vital in various fields. A photoluminescence (PL)- and mechanoluminescence (ML)-based multifunctional sensing platform is built by combining heterojunctioned ZnS/CaZnOS:Mn2+ mechano-photonic materials using a 3D-printing technique and fiber spinning. ML-active particles are embedded in micrometer-sized cellulose fibers for flexible optical devices capable of emitting light driven by mechanical force. Individually modified 3D-printed hard units that exhibit intense ML in response to mechanical deformation, such as impact and friction, are also fabricated. Importantly, they also allow low-pressure sensing up to ≈100 bar, a range previously inaccessible by any other optical sensing technique. Moreover, the developed optical manometer based on the PL of the materials demonstrates a superior high-pressure sensitivity of ≈6.20 nm GPa-1 . Using this sensing platform, four modes of temperature detection can be achieved: excitation-band spectral shifts, emission-band spectral shifts, bandwidth broadening, and lifetime shortening. This work supports the possibility of mass production of ML-active mechanical and optoelectronic parts integrated with scientific and industrial tools and apparatus.
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Affiliation(s)
- Teng Zheng
- School of Information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, China
| | - Marcin Runowski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, Poznań, 61-614, Poland
- Departamento de Física, IUdEA, IMN and MALTA Consolider Team, Universidad de La Laguna, San Cristóbal de La Laguna, Apartado de Correos 456, Santa Cruz de Tenerife, E-38200, Spain
| | - Inocencio R Martín
- Departamento de Física, IUdEA, IMN and MALTA Consolider Team, Universidad de La Laguna, San Cristóbal de La Laguna, Apartado de Correos 456, Santa Cruz de Tenerife, E-38200, Spain
| | - Kevin Soler-Carracedo
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, Poznań, 61-614, Poland
| | - Liang Peng
- School of Information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, China
| | - Małgorzata Skwierczyńska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, Poznań, 61-614, Poland
| | - Małgorzata Sójka
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Justyna Barzowska
- Institute of Experimental Physics, Faculty of Mathematics, Physics and Informatics, University of Gdansk, Wita Stwosza 57, Gdansk, 80-308, Poland
| | - Sebastian Mahlik
- Institute of Experimental Physics, Faculty of Mathematics, Physics and Informatics, University of Gdansk, Wita Stwosza 57, Gdansk, 80-308, Poland
| | - Hanoch Hemmerich
- Departamento de Física, IUdEA, IMN and MALTA Consolider Team, Universidad de La Laguna, San Cristóbal de La Laguna, Apartado de Correos 456, Santa Cruz de Tenerife, E-38200, Spain
| | - Fernando Rivera-López
- Departamento de Ingeniería Industrial, Escuela Superior de Ingeniería y Tecnología, Universidad de La Laguna, San Cristóbal de La Laguna, Apdo. 456, Santa Cruz de Tenerife, E-38200, Spain
| | - Piotr Kulpiński
- Faculty of Material Technologies and Textile Design, Department of Mechanical Engineering, Informatics and Chemistry of Polymer Materials, Lodz University of Technology, Żeromskiego 116, Lodz, 90-924, Poland
| | - Víctor Lavín
- Departamento de Física, IUdEA, IMN and MALTA Consolider Team, Universidad de La Laguna, San Cristóbal de La Laguna, Apartado de Correos 456, Santa Cruz de Tenerife, E-38200, Spain
| | - Daniel Alonso
- Departamento de Física, IUdEA, IMN and MALTA Consolider Team, Universidad de La Laguna, San Cristóbal de La Laguna, Apartado de Correos 456, Santa Cruz de Tenerife, E-38200, Spain
| | - Dengfeng Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
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43
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Oras E, Tõrv M, Johanson K, Rannamäe E, Poska A, Lõugas L, Lucquin A, Lundy J, Brown S, Chen S, Varul L, Haferberga V, Legzdiņa D, Zariņa G, Cramp L, Heyd V, Reay M, Pospieszny Ł, Robson HK, Nordqvist K, Heron C, Craig OE, Kriiska A. Parallel worlds and mixed economies: multi-proxy analysis reveals complex subsistence systems at the dawn of early farming in the northeast Baltic. R Soc Open Sci 2023; 10:230880. [PMID: 37800159 PMCID: PMC10548101 DOI: 10.1098/rsos.230880] [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: 06/22/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
The transition from foraging to farming was a key turning point in ancient socio-economies. Yet, the complexities and regional variations of this transformation are still poorly understood. This multi-proxy study provides a new understanding of the introduction and spread of early farming, challenging the notions of hierarchical economies. The most extensive biological and biomolecular dietary overview, combining zooarchaeological, archaeobotanical, dietary stable isotope and pottery lipid residue analyses is presented, to unravel the nature and extent of early farming in the 3rd millennium cal BCE in the northeast Baltic. Farming was introduced by incoming Corded Ware cultural groups (CWC), but some dietary segregation existed within these communities, with some having more access to domesticates, others incorporating more wild resources into their diet. The CWC groups coexisted in parallel with local hunter-fisher-gatherers (HFG) without any indication of the adoption of domesticates. There was no transition from foraging to farming in the 3rd millennium cal BCE in the NE Baltic. Instead, we see a complex system of parallel worlds with local HFGs continuing forager lifeways, and incoming farmers practising mixed economies, with the continuation of these subsistence strategies for at least a millennium after the first encounter with domesticated animals.
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Affiliation(s)
- Ester Oras
- Institute of Chemistry, University of Tartu, Ravila 14 a, 50411 Tartu, Estonia
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
- Swedish Collegium for Advanced Study (SCAS), Linneanum, Thunbergsvägen 2, 75238 Uppsala, Sweden
| | - Mari Tõrv
- Institute of Chemistry, University of Tartu, Ravila 14 a, 50411 Tartu, Estonia
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Kristiina Johanson
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Eve Rannamäe
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Anneli Poska
- Department of Geology, Tallinn University of Technology, Ehitajate Tee 5, 19086 Tallinn, Estonia
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Jasmine Lundy
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Samantha Brown
- Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Shidong Chen
- Institute of Chemistry, University of Tartu, Ravila 14 a, 50411 Tartu, Estonia
| | - Liivi Varul
- School of Humanities, Division of History, Tallinn University, Narva rd 25, 10120 Tallinn, Estonia
| | - Vanda Haferberga
- Institute of Latvian History, University of Latvia, Kalpaka blvd 4, LV-1050 Riga, Latvia
| | - Dardega Legzdiņa
- Institute of Latvian History, University of Latvia, Kalpaka blvd 4, LV-1050 Riga, Latvia
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Kalpaka blvd 4, LV-1050 Riga, Latvia
| | - Lucy Cramp
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, BS8 1UU Bristol, UK
| | - Volker Heyd
- Department of Cultures, University of Helsinki, Unioninkatu 38, 00014 Helsinki, Finland
| | - Michaela Reay
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, BS8 1TS Bristol, UK
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, BS8 1UU Bristol, UK
- Institute of Archaeology, University of Gdańsk, ul. Bielańska 5, 80-851 Gdańsk, Poland
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Kerkko Nordqvist
- Helsinki Collegium for Advanced Studies, University of Helsinki, Fabianinkatu 24, 00014 Helsinki, Finland
| | - Carl Heron
- Department of Scientific Research, The British Museum, WC1B 3DG London, UK
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Aivar Kriiska
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
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Tołkacz K, Kretschmer M, Nowak S, Mysłajek RW, Alsarraf M, Wężyk D, Bajer A. The first report on Hepatozoon canis in dogs and wolves in Poland: clinical and epidemiological features. Parasit Vectors 2023; 16:313. [PMID: 37667369 PMCID: PMC10476436 DOI: 10.1186/s13071-023-05928-5] [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: 05/27/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Canine hepatozoonosis caused by Hepatozoon canis is a common infection in dogs, with frequent case reports from the Mediterranean region and more recently from several Central European countries, such as Hungary and Germany. Despite the high prevalence of H. canis in red foxes, no infections have been reported to date in dogs in Poland. We describe here the first autochthonous cases of H. canis infection in dogs, including their clinical features, and report the prevalence of H. canis in grey wolves from different regions of Poland. METHODS Thin smears prepared from blood samples collected from dogs were evaluated by microscopic examination. A total of 60 wolves and 47 dogs were tested. Infections were confirmed by PCR and sequencing. RESULTS Gamonts of H. canis were found in > 50% of the neutrophils of two dogs and in < 10% of the neutrophils in another five dogs. Molecular typing by PCR sequencing of the 18S ribosomal RNA gene fragment confirmed infections in 11 dogs from different regions of Poland, in 2.7% of dogs attending veterinary practices in central Poland and in 35% of wolves from various geographical regions of Poland. Clinical features manifested mostly in older dogs, and the most common signs were anaemia and apathy. Young dogs usually remained asymptomatic. CONCLUSIONS This is the first report of H. canis infection in dogs and wolves in Poland. Although the exact vector of the parasite is not known, veterinary practitioners should be aware of this new parasitosis and should consider appropriate diagnostics to confirm/exclude this infection. Further studies are needed to understand the transmission routes of H. canis in domestic and wild canids in Poland.
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Affiliation(s)
- Katarzyna Tołkacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Str, 02-106 Warsaw, Poland
| | - Milena Kretschmer
- Vetlab Sp. Z O. O., Veterinary Diagnostic Laboratory, Wodzisławska Str 6, 52-017 Wrocław, Poland
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Mustafa Alsarraf
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dagmara Wężyk
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Bajer
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Sokolowska O, Rodziewicz-Lurzynska A, Pilch Z, Kedzierska H, Chlebowska-Tuz J, Sosnowska A, Szumera-Cieckiewicz A, Sokol K, Barankiewicz J, Salomon-Perzynski A, Ciepiela O, Lech-Maranda E, Golab J, Nowis D. Immune checkpoint inhibition improves antimyeloma activity of bortezomib and STING agonist combination in Vk*MYC preclinical model. Clin Exp Med 2023; 23:1563-1572. [PMID: 36044158 PMCID: PMC10460740 DOI: 10.1007/s10238-022-00878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/18/2022] [Indexed: 11/03/2022]
Abstract
Multiple myeloma (MM), a hematological malignancy of plasma cells, has remained incurable despite the development of novel therapies that improve patients' outcome. Recent evidence indicates that the stimulator of interferon genes (STING) pathway may represent a novel target for induction of antitumor immune response in multiple myeloma. Here, we investigated antitumor effects of STING agonist with bortezomib with or without checkpoint inhibitor in the treatment of MM. METHODS STING expression in bone marrow plasma cells of 58 MM patients was examined by immunohistochemical staining. The effectiveness of the proposed therapy was evaluated in vivo in a syngeneic transplantable mouse model of MM (Vĸ*MYC) in immunocompetent mice. Flow cytometry was used to assess tumor burden and investigate activation of immune response against MM. ELISA was performed to measure serum inflammatory cytokines concentrations upon treatment. RESULTS Combining a STING agonist [2'3'-cGAM(PS)2] with bortezomib significantly decreased tumor burden and improved the survival of treated mice compared to either of the compounds used alone. The combination treatment led to secretion of pro-inflammatory cytokines and increased the percentage of neutrophils, activated dendritic cells and T cells in the tumor microenvironment. However, it resulted also in increased expression of PD-L1 on the surface of the immune cells. Addition of anti-PD1 antibody further potentiated the therapeutic effects. CONCLUSIONS Our findings indicate high antimyeloma efficacy of the three-drug regimen comprising bortezomib, STING agonist, and a checkpoint inhibitor.
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Affiliation(s)
- Olga Sokolowska
- Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, Banacha, 2C, 02-097, Warsaw, Poland
| | - Anna Rodziewicz-Lurzynska
- Central Laboratory, University Clinical Center of Medical University of Warsaw, Banacha 1A, 02-097, Warsaw, Poland
| | - Zofia Pilch
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097, Warsaw, Poland
| | - Hanna Kedzierska
- Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, Banacha, 2C, 02-097, Warsaw, Poland
| | - Justyna Chlebowska-Tuz
- Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, Banacha, 2C, 02-097, Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097, Warsaw, Poland
| | - Anna Sosnowska
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097, Warsaw, Poland
| | - Anna Szumera-Cieckiewicz
- Department of Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Diagnostic Hematology Department, Institute of Hematology and Transfusion Medicine, Indiri Ghandi 14, 02-776, Warsaw, Poland
| | - Kamil Sokol
- Diagnostic Hematology Department, Institute of Hematology and Transfusion Medicine, Indiri Ghandi 14, 02-776, Warsaw, Poland
| | - Joanna Barankiewicz
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Indiri Ghandi 14, 02-776, Warsaw, Poland
| | - Aleksander Salomon-Perzynski
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Indiri Ghandi 14, 02-776, Warsaw, Poland
| | - Olga Ciepiela
- Department of Laboratory Medicine, Medical University of Warsaw, Banacha 1A, 02-097, Warsaw, Poland
| | - Ewa Lech-Maranda
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Indiri Ghandi 14, 02-776, Warsaw, Poland
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097, Warsaw, Poland
- Centre of Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097, Warsaw, Poland
| | - Dominika Nowis
- Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, Banacha, 2C, 02-097, Warsaw, Poland.
- Laboratory of Experimental Medicine, Medical University of Warsaw, Nielubowicza 5, 02-097, Warsaw, Poland.
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Sarycheva T, Čapková N, Pająk A, Tamošiūnas A, Bobák M, Pikhart H. Can spirometry improve the performance of cardiovascular risk model in high-risk Eastern European countries? Front Cardiovasc Med 2023; 10:1228807. [PMID: 37711557 PMCID: PMC10497938 DOI: 10.3389/fcvm.2023.1228807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023] Open
Abstract
Aims Impaired lung function has been strongly associated with cardiovascular disease (CVD) events. We aimed to assess the additive prognostic value of spirometry indices to the risk estimation of CVD events in Eastern European populations in this study. Methods We randomly selected 14,061 individuals with a mean age of 59 ± 7.3 years without a previous history of cardiovascular and pulmonary diseases from population registers in the Czechia, Poland, and Lithuania. Predictive values of standardised Z-scores of forced expiratory volume measured in 1 s (FEV1), forced vital capacity (FVC), and FEV1 divided by height cubed (FEV1/ht3) were tested. Cox proportional hazards models were used to estimate hazard ratios (HRs) of CVD events of various spirometry indices over the Framingham Risk Score (FRS) model. The model performance was evaluated using Harrell's C-statistics, likelihood ratio tests, and Bayesian information criterion. Results All spirometry indices had a strong linear relation with the incidence of CVD events (HR ranged from 1.10 to 1.12 between indices). The model stratified by FEV1/ht3 tertiles had a stronger link with CVD events than FEV1 and FVC. The risk of CVD event for the lowest vs. highest FEV1/ht3 tertile among people with low FRS was higher (HR: 2.35; 95% confidence interval: 1.96-2.81) than among those with high FRS. The addition of spirometry indices showed a small but statistically significant improvement of the FRS model. Conclusions The addition of spirometry indices might improve the prediction of incident CVD events particularly in the low-risk group. FEV1/ht3 is a more sensitive predictor compared to other spirometry indices.
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Affiliation(s)
| | - Naděžda Čapková
- Environmental and Population Health Monitoring Centre, The National Institute of Public Health (NIPH), Prague, Czechia
| | - Andrzej Pająk
- Department of Epidemiology and Population Studies, Faculty of Health Sciences, Institute of Public Health, Jagiellonian University Medical College, Krakow, Poland
| | - Abdonas Tamošiūnas
- Laboratory of Population Research, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Martin Bobák
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
- Research Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Hynek Pikhart
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
- Research Department of Epidemiology and Public Health, University College London, London, United Kingdom
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Balazy K, Trudnowska E, Wojczulanis-Jakubas K, Jakubas D, Præbel K, Choquet M, Brandner MM, Schultz M, Bitz-Thorsen J, Boehnke R, Szeligowska M, Descamps S, Strøm H, Błachowiak-Samołyk K. Molecular tools prove little auks from Svalbard are extremely selective for Calanus glacialis even when exposed to Atlantification. Sci Rep 2023; 13:13647. [PMID: 37607972 PMCID: PMC10444800 DOI: 10.1038/s41598-023-40131-7] [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: 01/05/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Two Calanus species, C. glacialis and C. finmarchicus, due to different life strategies and environmental preferences act as an ecological indicators of Arctic Atlantification. Their high lipid content makes them important food source for higher trophic levels of Arctic ecosystems including the most abundant Northern Hemisphere's seabird, the little auk (Alle alle). Recent studies indicate a critical need for the use of molecular methods to reliably identify these two sympatric Calanus species. We performed genetic and morphology-based identification of 2600 Calanus individuals collected in little auks foraging grounds and diet in summer seasons 2019-2021 in regions of Svalbard with varying levels of Atlantification. Genetic identification proved that 40% of Calanus individuals were wrongly classified as C. finmarchicus according to morphology-based identification in both types of samples. The diet of little auks consisted almost entirely of C. glacialis even in more Atlantified regions. Due to the substantial bias in morphology-based identification, we expect that the scale of the northern expansion of boreal C. finmarchicus may have been largely overestimated and that higher costs for birds exposed to Atlantification could be mostly driven by a decrease in the size of C. glacialis rather than by shift from C. glacialis to C. finmarchicus.
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Affiliation(s)
- Kaja Balazy
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland.
| | - Emilia Trudnowska
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
| | | | - Dariusz Jakubas
- Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdansk, 80-309, Gdansk, Poland
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Melissa M Brandner
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mads Schultz
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Julie Bitz-Thorsen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Rafał Boehnke
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
| | - Marlena Szeligowska
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
| | | | - Hallvard Strøm
- Norwegian Polar Institute (NPI), Fram Centre, 9296, Tromsø, Norway
| | - Katarzyna Błachowiak-Samołyk
- Department of Marine Ecology, Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-222, Sopot, Poland
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Kharchenko S, Samborski S, Kharchenko F, Mitura A, Paśnik J, Korzec I. Identification of the Natural Frequencies of Oscillations of Perforated Vibrosurfaces with Holes of Complex Geometry. Materials (Basel) 2023; 16:5735. [PMID: 37687428 PMCID: PMC10489056 DOI: 10.3390/ma16175735] [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: 07/12/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023]
Abstract
The reliability of perforated vibrosurfaces is one of the main parameters of the efficiency of their operation in many technological processes. Existing methods for studying vibrosurfaces with standard single holes and the corresponding results cannot be used to study the reliability of vibration surfaces with holes of complex geometric shapes. The proposed method is based on the experimental modal identification of the parameters of natural oscillations, the parallel creation of a numerical model using the finite element method, and the comparison of the results. Three vibrosurfaces were investigated: solid without holes, perforated with standard round holes, perforated with holes in the form of a five-petal epicycloid. As a result of experiments, the divergence of natural vibrations of perforated surfaces depending on the side of the punch and matrix during their technological production by pressing was established. The result of the research was a refined adequate numerical model that takes into account the presence of holes in complex geometric shapes. A methodology has been developed, and analytical expressions with perforation coefficients have been obtained, which allow obtaining values of natural oscillations of vibration surfaces depending on the properties of metal, boundary conditions, and structural and kinematic parameters.
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Affiliation(s)
- Serhii Kharchenko
- Department of Applied Mechanics, Lublin University of Technology, 20-618 Lublin, Poland
| | - Sylwester Samborski
- Department of Fundamentals of Production Engineering, Lublin University of Technology, 20-618 Lublin, Poland
| | - Farida Kharchenko
- Department of Agricultural Engineering, Sumy National Agrarian University, 40-021 Sumy, Ukraine
| | - Andrzej Mitura
- Department of Applied Mechanics, Lublin University of Technology, 20-618 Lublin, Poland
| | - Jakub Paśnik
- Department of Machine Design and Mechatronics, Lublin University of Technology, 20-618 Lublin, Poland
| | - Izabela Korzec
- Department of Applied Mechanics, Lublin University of Technology, 20-618 Lublin, Poland
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Kałafut J, Czerwonka A, Czapla K, Przybyszewska-Podstawka A, Hermanowicz JM, Rivero-Müller A, Borkiewicz L. Regulation of Notch1 Signalling by Long Non-Coding RNAs in Cancers and Other Health Disorders. Int J Mol Sci 2023; 24:12579. [PMID: 37628760 PMCID: PMC10454443 DOI: 10.3390/ijms241612579] [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: 07/12/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Notch1 signalling plays a multifaceted role in tissue development and homeostasis. Currently, due to the pivotal role of Notch1 signalling, the relationship between NOTCH1 expression and the development of health disorders is being intensively studied. Nevertheless, Notch1 signalling is not only controlled at the transcriptional level but also by a variety of post-translational events. First is the ligand-dependent mechanical activation of NOTCH receptors and then the intracellular crosstalk with other signalling molecules-among those are long non-coding RNAs (lncRNAs). In this review, we provide a detailed overview of the specific role of lncRNAs in the modulation of Notch1 signalling, from expression to activity, and their connection with the development of health disorders, especially cancers.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Karolina Czapla
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland;
- Department of Clinical Pharmacy, Medical University of Bialystok, Waszyngtona 15, 15-274 Bialystok, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
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50
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Witkowska M, Jedrzejczak RP, Joachimiak A, Cavdar O, Malankowska A, Skowron PM, Zylicz-Stachula A. Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site. Microb Cell Fact 2023; 22:134. [PMID: 37479997 PMCID: PMC10362691 DOI: 10.1186/s12934-023-02127-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. RESULTS Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. CONCLUSION The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.
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Affiliation(s)
- Malgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Robert P Jedrzejczak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Onur Cavdar
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Anna Malankowska
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland.
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