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Gonzalez-Santamarta M, Ceccato L, Carvalho AS, Rain JC, Matthiesen R, Rodriguez MS. Isolation and Mass Spectrometry Identification of K48 and K63 Ubiquitin Proteome Using Chain-Specific Nanobodies. Methods Mol Biol 2023; 2602:125-136. [PMID: 36446971 DOI: 10.1007/978-1-0716-2859-1_9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein ubiquitylation is an essential mechanism regulating almost all cellular functions in eukaryotes. The understanding of the role of distinct ubiquitin chains in different cellular processes is essential to identify biomarkers for disease diagnosis and prognosis but also to open new therapeutic possibilities. The high complexity of ubiquitin chains complicates this analysis, and multiple strategies have been developed over the last decades. Here, we report a protocol for the isolation and identification of K48 and K63 ubiquitin chains using chain-specific nanobodies associated to mass spectrometry. Different steps were optimized to increase the purification yield and reduce the binding on nonspecific proteins. The resulting protocol allows the enrichment of ubiquitin chain-specific targets from mammalian cells.
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Affiliation(s)
- Maria Gonzalez-Santamarta
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, Toulouse, France
| | - Laurie Ceccato
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, Toulouse, France
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | | | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, Toulouse, France.
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152
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Bagheralmoosavi S, Gholami P, Amini M, Alizadeh M, Yaghmaei M, Tavakkoli S, Salari S, Jeddi-Tehrani M, Ghasempour A, Gilany K, Shabani M. Proteome Analysis of Adult Acute Lymphoblastic Leukemia by Two-dimensional Blue Native/Sodium Dodecyl Sulfate Gel Electrophoresis. Avicenna J Med Biotechnol 2023; 15:21-27. [PMID: 36789118 PMCID: PMC9895978 DOI: 10.18502/ajmb.v15i1.11421] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/26/2022] [Indexed: 12/27/2022] Open
Abstract
Background Despite the significant progress in the treatment of Acute Lymphoblastic Leukemia (ALL) in children, it still remains as one of the most challenging malignancies in adults. Identification of new biomarkers may improve the management of adult ALL. Proteins expressed on the cell surface can be considered as disease-associated biomarkers with potential for diagnosis and targeted therapies. Thus, membrane proteome studies give essential information about the disease-related biomarkers. Methods We applied 2-dimensional blue-native SDS-PAGE technique followed by MALDI-TOF/TOF-mass spectrometry to study the cell membrane proteome of peripheral blood mononuclear cells of adult B-ALL patients in comparison to that of the healthy controls. Results Sixty seven differentially expressed protein spots were detected, among them 52 proteins were found to be up-regulated but the other 15 proteins were down-regulated in B-ALL. Five differentially expressed proteins, involved in energy metabolism pathways, were detected in B-ALL patients compared to the healthy control group. Conclusion Differentially expressed proteins provide an insight into the molecular biology of B-ALL. Further studies must be done to confirm our data to be considered as potential targets for detection and treatment of B-ALL.
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Affiliation(s)
- Servin Bagheralmoosavi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parastou Gholami
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Amini
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mahdi Alizadeh
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Marjan Yaghmaei
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sahar Tavakkoli
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sina Salari
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Alireza Ghasempour
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mahdi Shabani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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153
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Sarkar M, Saha S. Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome. Methods Mol Biol 2023; 2627:265-299. [PMID: 36959453 DOI: 10.1007/978-1-0716-2974-1_15] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
COronaVIrus Disease 19 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a group of beta coronaviruses, SARS-CoV-2. The SARS-CoV-2 virus is similar to previous SARS- and MERS-causing strains and has infected nearly six hundred and fifty million people all over the globe, while the death toll has crossed the six million mark (as of December, 2022). In this chapter, we look at how computational modeling approaches of the viral proteins could help us understand the various processes in the viral life cycle inside the host, an understanding of which might provide key insights in mitigating this and future threats. This understanding helps us identify key targets for the purpose of drug discovery and vaccine development.
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Affiliation(s)
- Manish Sarkar
- Hochschule für Technik und Wirtschaft (HTW) Berlin, Berlin, Germany
- MedInsights SAS, Paris, France
| | - Soham Saha
- MedInsights, Veuilly la Poterie, France.
- MedInsights SAS, Paris, France.
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154
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Walls D, Cooney G, Loughran ST. A Synopsis of Proteins and Their Purification. Methods Mol Biol 2023; 2699:1-14. [PMID: 37646990 DOI: 10.1007/978-1-0716-3362-5_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The goal of protein purification is to separate a specific protein from all other biomolecules. Classical chromatographic procedures have been designed to exploit particular distinguishing features of individual target proteins, such as size, shape, physicochemical properties, and binding affinity. Advances in molecular biology and bioinformatics have positively contributed at every level to the challenge of purifying individual proteins and more recently have led to the development of high-throughput proteomic platforms. In this chapter, a synopsis of advancements in the field of protein chromatography is presented, with reference to the principal tools and resources that are available to assist with protein purification strategies.
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Affiliation(s)
- Dermot Walls
- School of Biotechnology , Dublin City University, Dublin, Ireland
| | - Gary Cooney
- School of Biotechnology , Dublin City University, Dublin, Ireland
| | - Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Ireland.
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155
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Santos MA, Silva FL, Lira BOV, Cardozo Fh JL, Vasconcelos AG, Araujo AR, Murad AM, Garay AV, Freitas SM, Leite JRSA, Bloch C, Ramada MHS, de Oliveira AL, Brand GD. Probing human proteins for short encrypted antimicrobial peptides reveals Hs10, a peptide with selective activity for gram-negative bacteria. Biochim Biophys Acta Gen Subj 2023; 1867:130265. [PMID: 36280021 DOI: 10.1016/j.bbagen.2022.130265] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Some cationic and amphiphilic α-helical segments of proteins adsorb to prokaryotic membranes when synthesized as individual polypeptide sequences, resulting in broad and potent antimicrobial activity. However, amphiphilicity, a determinant physicochemical property for peptide-membrane interactions, can also be observed in some β-sheets. METHODS The software Kamal was used to scan the human reference proteome for short (7-11 amino acid residues) cationic and amphiphilic protein segments with the characteristic periodicity of β-sheets. Some of the uncovered peptides were chemically synthesized, and antimicrobial assays were conducted. Biophysical techniques were used to probe the molecular interaction of one peptide with phospholipid vesicles, lipopolysaccharides (LPS) and the bacterium Escherichia coli. RESULTS Thousands of compatible segments were found in human proteins, five were synthesized, and three presented antimicrobial activity in the micromolar range. Hs10, a nonapeptide fragment of the Complement C3 protein, could inhibit only the growth of tested Gram-negative microorganisms, presenting also little cytotoxicity to human fibroblasts. Hs10 interacted with LPS while transitioning from an unstructured segment to a β-sheet and increased the hydrodynamic radius of LPS particles. This peptide also promoted morphological alterations in E. coli cells. CONCLUSIONS Data presented herein introduce yet another molecular template to probe proteins in search for encrypted membrane-active segments and demonstrates that, using this approach, short peptides with low cytotoxicity and high selectivity to prokaryotic cells might be obtained. GENERAL SIGNIFICANCE This work widens the biotechnological potential of the human proteome as a source of antimicrobial peptides with application in human health.
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Affiliation(s)
- Michele A Santos
- Laboratório de Ressonância Magnética Nuclear, LRMN, Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil; Laboratório de Síntese e Análise de Biomoléculas, LSAB, Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil
| | - Fernanda L Silva
- Laboratório de Síntese e Análise de Biomoléculas, LSAB, Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil
| | - Bianca O V Lira
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - José L Cardozo Fh
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Andreanne G Vasconcelos
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Campus Universitário Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brazil
| | - Alyne R Araujo
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Universidade Federal do Piauí, Parnaíba, PI, Brazil
| | - André M Murad
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Aisel V Garay
- Laboratório de Biofísica Molecular, Instituto de Biologia, Universidade de Brasília (IB-CEL/UnB), Campus Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - Sonia M Freitas
- Laboratório de Biofísica Molecular, Instituto de Biologia, Universidade de Brasília (IB-CEL/UnB), Campus Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - José Roberto S A Leite
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Campus Universitário Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brazil
| | - Carlos Bloch
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Marcelo H S Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Aline Lima de Oliveira
- Laboratório de Ressonância Magnética Nuclear, LRMN, Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil
| | - Guilherme D Brand
- Laboratório de Síntese e Análise de Biomoléculas, LSAB, Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil.
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156
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Mielecki D, Grzesiuk E, Bednarska A, Garbicz D, Świderska B, Grzesiuk M. Contamination of aquatic environment with anticancer reagents influences Daphnia magna - Ecotoxicogenomics approach. Ecotoxicol Environ Saf 2023; 249:114372. [PMID: 36508828 DOI: 10.1016/j.ecoenv.2022.114372] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Pharmaceuticals used in human medicine contaminate freshwater ecosystems. Chemotherapeutics applied in cancer treatment are found in freshwaters at low concentrations (in the range of ng L-1) which, however, can be toxic or mutagenic to aquatic organisms. The aim of this study was to determine the impact of the alkylating/crosslinking anticancer agents, cyclophosphamide (CP) and cisplatin (CDDP), at the concentration detected in water, on Daphnia magna life history, transcriptome, and proteome. This filter feeding cladoceran is an important member of the aquatic food webs controlling algal biomass and forming basic food for planktivorous fish. Here, observations of the D. magna growth rate, age at first reproduction, and the number of eggs produced were performed in the presence of CP or CDDP. The D. magna proteins and RNA were isolated and analysed by mass spectrometry and the mRNA-seq method, respectively. Five generations of contact with the pharmaceuticals in question significantly influenced the D. magna life history parameters with the growth rate and number of laid eggs decreased, whereas age at first reproduction was increased. A decrease in survivorship was observed when daphnids were exposed to CP. These changes are the result of modifications in the gene/transcript expression followed by differences in the proteome profile in comparison to the untreated control. The proteome changes were generally in accordance with the modified transcriptome. The ecotoxicogenomics approach makes it possible to get closer to a complete picture of the influence of CP and CDDP on Daphnia. We have gathered evidence that animals in the presence of anticancer pharmaceuticals attempt to cope with permanent stress by changing their proteome and transcriptome profile. Additionally, our analyses indicate that CDDP showed a stronger effect on tested organisms than CP.
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Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; Department of Immunohematology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Anna Bednarska
- Department of Hydrobiology, Faculty of Biology, University of Warsaw, Poland
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, Warsaw, Poland
| | - Bianka Świderska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Malgorzata Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; Department of Hydrobiology, Faculty of Biology, University of Warsaw, Poland; Department of Biochemistry and Microbiology, Institute of Biology; Warsaw University of Life Sciences (SGGW), Warsaw, Poland.
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157
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Wiśniewska K, Siatkowska M, Komorowski P, Napieralska K, Kasperkiewicz K, Surmiak-Stalmach K, Wilczek G. Effects of chronic exposure to cadmium and copper on the proteome profile of hemolymph in false widow spider Steatoda grossa (Theridiidae). Ecotoxicol Environ Saf 2023; 249:114448. [PMID: 38321667 DOI: 10.1016/j.ecoenv.2022.114448] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/28/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2024]
Abstract
The aim of this study was to evaluate the quantitative and qualitative changes in the proteome of the hemolymph of female Steatoda grossa spiders (Theridiidae) that were chronically exposed to cadmium and copper in food and were additionally immunostimulated (phorbol 12-myristate 13-acetate (PMA); bacterial suspensions: Staphylococcus aureus (G+), Pseudomonas fluorescens (G-). It was found that the expression of nearly 90 proteins was altered in cadmium-intoxicated spiders and more than 60 in copper-exposed individuals. Regardless of the type of metal used, these proteins were mainly overexpressed in the hemolymph of the exposed spiders. On the other hand, immunostimulation did not significantly change the number of proteins with altered expression in metal-intoxicated individuals. Hemocyanin (Hc) was found to be the most abundant of the proteins identified with altered expression. In copper-intoxicated spiders, immunostimulation increased the expression of A-, E-, F-, and G-chain-containing proteins, while in the case of cadmium-intoxicates spiders, it decreased the expression of E- and A-chain-containing Hc and increased the expression of G-chain-containing Hc. Regardless of the type of metal and immunostimulant used, there was an increase in the expression of actin. In addition, cadmium increased the expression of cullin, vimentin, and ceruloplasmin. The changes observed in the expression of hemolymph proteins indicate their protective function in S. grossa (Theridiidae) spiders under conditions of metal exposure.
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Affiliation(s)
- Kamila Wiśniewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Małgorzata Siatkowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland; Laboratory of Molecular and Nanostructural Biophysics, Bionanopark Ltd. Dubois 114/116, 93-465 Łódź, Poland
| | - Piotr Komorowski
- Laboratory of Molecular and Nanostructural Biophysics, Bionanopark Ltd. Dubois 114/116, 93-465 Łódź, Poland; Department of Biophysics, Institute of Materials Science, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Kinga Napieralska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland; Laboratory of Molecular and Nanostructural Biophysics, Bionanopark Ltd. Dubois 114/116, 93-465 Łódź, Poland
| | - Katarzyna Kasperkiewicz
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Kinga Surmiak-Stalmach
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Grażyna Wilczek
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland.
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158
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Perez R, Benbachir M, Decroo C, Mascolo C, Wattiez R, Aron S. Cataglyphis desert ants use distinct behavioral and physiological adaptations to cope with extreme thermal conditions. J Therm Biol 2023; 111:103397. [PMID: 36585078 DOI: 10.1016/j.jtherbio.2022.103397] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Some ant species live in hot and arid environments, such as deserts and savannas. Worker polymorphism-variation in worker size and/or morphology within colonies-is adaptive in such ecosystems because it enhances resistance to heat stress and increases the efficiency of resource exploitation. However, species with small, monomorphic workers are also frequently found in these environments. How species with distinct worker size and degrees of polymorphism deal with such stressful environments remains poorly studied. We investigated the behavioral, physiological, and molecular adaptations that may enhance heat and desiccation tolerance in two sympatric species of Cataglyphis desert ants that differ dramatically in worker size and polymorphism: C. viatica is polymorphic, while C. cubica is small and monomorphic. We found that worker size, water content, water loss, and protein regulation play a key role in thermal resistance. (i) Large C. viatica workers better tolerated heat and desiccation stress than did small C. viatica or C. cubica workers. The former had greater water content and lost proportionally less water to evaporation under thermal stress. (ii) Despite their similar size distribution, workers of C. cubica are more heat tolerant than small C. viatica. This higher degree of tolerance likely stemmed from C. cubica workers having greater relative water content. (iii) Under thermal stress, small C. viatica workers metabolized larger quantities of fat and differentially expressed proteins involved in cellular homeostasis. In contrast, C. cubica downregulated the expression of numerous proteins involved in mitochondrial respiration likely reducing ROS accumulation. (iv) Consistent with these results, large C. viatica workers remained active throughout the day; C. cubica workers displayed a bimodal activity pattern, and small C. viatica remained poorly active outside the nest. Our study shows that ecologically similar ant species with different degrees of worker size polymorphism evolved distinct strategies for coping with extreme heat conditions.
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Affiliation(s)
- Rémy Perez
- Department of Evolutionary Biology & Ecology, Université Libre de Bruxelles, B-1050, Brussels, Belgium.
| | - Mohammed Benbachir
- Department of Evolutionary Biology & Ecology, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Corentin Decroo
- Department of Proteomics and Microbiology, Université de Mons, B-7000, Mons, Belgium
| | - Cyril Mascolo
- Department of Proteomics and Microbiology, Université de Mons, B-7000, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Université de Mons, B-7000, Mons, Belgium
| | - Serge Aron
- Department of Evolutionary Biology & Ecology, Université Libre de Bruxelles, B-1050, Brussels, Belgium
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159
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Maruyama Y, Seki T, Ando S, Tanabe H, Mori H. Analysis of IGHA1 and other salivary proteins post half marathon in female participants. PeerJ 2023; 11:e15075. [PMID: 37193030 PMCID: PMC10183162 DOI: 10.7717/peerj.15075] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 05/18/2023] Open
Abstract
Background High-intensity exercise (HIE), such as that in marathons and triathlons, suppresses transient local and systemic immunity. Serum and salivary immunoglobulin heavy constant alpha 1 (IGHA1) are major markers of immunosuppression by HIE. Although much is known about the systemic immunosuppressive response, little is known about its local response in the oral cavity, lungs, bronchial tubes, and skin. The oral cavity allows bacteria or viruses to enter the body. Saliva covers the epidermis of the oral cavity and plays an important role in the local stress response by preventing infection. In this study, we examined the properties of saliva secreted during the local stress response for half-marathon (HM) induced IGHA1 protein expression using quantitative proteomics. Methods The Exercise Group (ExG) (19 healthy female university students) participated in a HM race. The Non-Exercise Group (NExG) (16 healthy female university students) did not participate in the ExG. The ExG saliva samples were collected 1 h pre and 2 h and 4 h post-HM. The NExG saliva samples were collected at the same time intervals. The saliva volume, protein concentration, and relative IGHA1 expression were analyzed. In addition, 1 h pre and 2 h post- HM saliva samples were analyzed by iTRAQ. The identified factors in iTRAQ were analyzed for the ExG and the NExG using western blotting. Results We identified kallikrein 1 (KLK1), immunoglobulin kappa chain (IgK), and cystatin S (CST4) as suppression factors, as well as IGHA1, which has been reported to be an immunological stress marker. IGHA1 (p = 0.003), KLK1 (p = 0.011), IGK (p = 0.002), and CST4 (p = 0.003) were suppressed 2 h post-HM compared with their levels pre HM, and IGHA1 (p < 0.001), KLK1 (p = 0.004), and CST4 (p = 0.006) were suppressed 4 h post-HM. There was also a positive correlation between IGHA1, IGK, and CST4 levels at 2 and 4 h post-HM. In addition, KLK1 and IGK levels at 2 h post-HM were positively correlated. Conclusion Our study demonstrated that the salivary proteome is regulated, and antimicrobial proteins are suppressed post-HM. These results suggest that oral immunity was transiently suppressed post-HM. The positive correlation of each protein at 2 and 4 h post-HM suggests that the suppressed state was similarly regulated up to 4 h after a HM. The proteins identified in this study may have applications as stress markers for recreational runners and individuals who perform moderate to HIE on a regular basis.
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Affiliation(s)
- Yosuke Maruyama
- Faculty of Health and Welfare Science Department of Nutritional Sciences, Nayoro City University, Nayoro, Hokkaido, Japan
| | - Tomoaki Seki
- National Institute of Fitness and Sports Kanoya, Kanoya, Kagoshima, Japan
| | - Seiichi Ando
- Clinical Nutrition and Internal Medicine, Kobe Women’s University, Kobe, Hyogo, Japan
| | - Hiroki Tanabe
- Faculty of Health and Welfare Science Department of Nutritional Sciences, Nayoro City University, Nayoro, Hokkaido, Japan
| | - Hitoshi Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
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Dang K, Farooq HMU, Dong J, Yang H, Kong Y, Wang H, Jiang S, Gao Y, Qian A. Transcriptomic and proteomic time-course analyses based on Metascape reveal mechanisms against muscle atrophy in hibernating Spermophilus dauricus. Comp Biochem Physiol A Mol Integr Physiol 2023; 275:111336. [PMID: 36280225 DOI: 10.1016/j.cbpa.2022.111336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/19/2022]
Abstract
Hibernating Spermophilus dauricus is resistant to muscle atrophy. Comprehensive transcriptome and proteome time-course analyses based on Metascape can further reveal the underlying processes (pre-hibernation stage, PRE; torpor stage, TOR; interbout arousal stage, IBA; and post-hibernation stage, POST). Transcriptome analysis showed that the cellular responses to growth factor stimulus and discrete oxygen levels continuously changed during hibernation. Proteomic analysis showed that neutrophil degranulation, sulfur compound metabolic process, and generation of precursor metabolites and energy continuously changed during hibernation. Molecular complex detection (MCODE) analysis in both transcriptome and proteome indicated that smooth muscle contraction was involved in the POST versus IBA stage, and peroxisome proliferator-activated receptor delta (Ppard), Myc proto-oncogene (Myc), Sp1 transcription factor (Sp1), and nuclear factor Kappa B subunit 1 (NFκB1) are the common TFs during the hibernation process. Integrated transcriptome and proteome analyses found 18 molecules in the TOR versus PRE stage, 1 molecule in the IBA versus TOR stage, and 16 molecules in the POST versus IBA stage. Among these molecules, carnitine palmitoyltransferase 1A (Cpt1a), SET and MYND domain containing 2 (Smyd2), four and a half LIM domains 1(Fhl1), reactive oxygen species modulator 1 (Romo1), and translocase of the inner mitochondrial membrane 50 (Timm50) were testified by Western blot. In conclusion, novel muscle atrophy resistance mechanisms can be deciphered by time-course transcriptome and proteome analyses based on Metascape.
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Hopkins K, Price B, Ziogas J, Adamides A, Mangum J. Comparative proteomic analysis of ventricular and cisternal cerebrospinal fluid in haemorrhagic stroke patients. J Clin Neurosci 2023; 107:84-90. [PMID: 36525746 DOI: 10.1016/j.jocn.2022.11.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Analysis of cerebrospinal fluid (CSF) using mass spectrometry is a relatively novel analytical tool, and comparisons of ventricular and cisternal proteomes are yet to be performed. This may have implications for clinical medicine, particularly in demonstrating continuity of the ventricular system with preserved flow in the presence of ventricular blood. Other uses include the identification of novel biomarkers, including for diagnosis of subarachnoid haemorrhage and of aetiology. The primary objective was therefore to characterise and compare the proteomes of ventricular and CSF after haemorrhagic stroke. METHODS Paired CSF samples were prospectively collected from the optico-carotid cistern and the frontal horn of the lateral ventricle at the time of craniotomy and clipping in 8 patients with haemorrhagic stroke. Six patients had an aneurysmal subarachnoid haemorrhage (aSAH) from a ruptured saccular aneurysm, one patient had an aSAH after rupture of a mycotic aneurysm and one patient had a spontaneous intracerebral haemorrhage (IPH) with an adjacent unruptured saccular aneurysm. Samples were processed and proteins identified and quantified using data-dependent liquid chromatography tandem mass spectrometry (DDA LC-MSMS). RESULTS There was no systematic difference between the cisternal and ventricular proteomes. However, blinded principal component analysis (PCA) of the cisternal and ventricular samples separated patients according to pathophysiology. Additionally CSF D-Dimer levels were not detected in the IPH patient but were reliably measured in aSAH patients. CONCLUSIONS Ventricular CSF is representative of cisternal CSF after aSAH. CSF proteomic PCA analysis can distinguish between haemorrhage types. CSF D-dimer levels may represent a novel diagnostic marker for aSAH. Label free DDA LC-MSMS CSF analysis may inform possible biomarkers.
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Affiliation(s)
- Katherine Hopkins
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin Price
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia; Department of Neurosurgery, The Royal Melbourne Hospital, Melbourne, VIC, Australia.
| | - James Ziogas
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Alexios Adamides
- Department of Neurosurgery, The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Jonathan Mangum
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
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162
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Anrather D, Polakova SB, Cipak L, Gregan J. SILAC-Based Proteomic Analysis of Meiosis in the Fission Yeast Schizosaccharomyces pombe. Methods Mol Biol 2023; 2603:19-29. [PMID: 36370267 DOI: 10.1007/978-1-0716-2863-8_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) provides a powerful tool to quantify proteins and posttranslational modifications. Here we describe how to apply SILAC for protein identification and quantification in synchronous meiotic cultures induced by inactivation of the Pat1 kinase in the fission yeast Schizosaccharomyces pombe.
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Affiliation(s)
- Dorothea Anrather
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria.
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia.
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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163
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Lv B, Peng Y, Peng YD, Wang Z, Song QS. Integrated transcriptome and proteome unveiled distinct toxicological effects of long-term cadmium pollution on the silk glands of Pardosa pseudoannulata. Sci Total Environ 2023; 854:158841. [PMID: 36116647 DOI: 10.1016/j.scitotenv.2022.158841] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) induces severe soil pollution worldwide and exerts adverse effects on paddy field arthropods. Spiders grant a novel perspective to assess the Cd-induced toxicity, yet the impacts of long-term Cd stress on spider silk glands and its underlying mechanism remain elusive. The study showed that Cd stress enervated the antioxidant system in the spider Pardosa pseudoannulata, manifested as the decreases of glutathione peroxidase and peroxidase, and the increase of malonaldehyde (p < 0.05). In addition, a total of 1459 differentially expressed genes (DEGs) and 404 differentially expressed proteins (DEPs) were obtained from the silk glands' transcriptome and proteome. DEGs and DEPs encoding spidroin (e.g., tubuliform spidroin and ampullate spidroin) and amino acids metabolism (e.g., alanine, proline, and glycine) were distinctively down-regulated. Further enrichment analysis verified that Cd stress could inhibit amino acid metabolism via the down-regulation of several key enzymes, including glutathione synthase, methylthioadenosine phosphorylase, S-adenosylmethionine synthetase, etc. In addition, the hedgehog signaling pathway regulating cellular growth and development was down-regulated under Cd stress. A protein-protein interaction network showed that long-term Cd stress could inhibit some key biological processes in the silk glands, including peptide biosynthetic process and cytoskeleton part. Collectively, this comprehensive study established an effective animal detection model for evaluating Cd-induced toxicity, presented key biomarkers for further validation, and provided novel insights to investigate the molecular mechanisms of spiders to Cd pollution.
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Affiliation(s)
- Bo Lv
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China; Division of Plant Science and Technology, University of Missouri, 65211 Columbia, USA
| | - Yong Peng
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China
| | - Yuan-de Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, Hunan, China
| | - Zhi Wang
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
| | - Qi-Sheng Song
- Division of Plant Science and Technology, University of Missouri, 65211 Columbia, USA.
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Freitag L, Spinell T, Kröger A, Würfl G, Lauseker M, Hickel R, Kebschull M. Dental implant material related changes in molecular signatures in peri-implantitis - A systematic review and integrative analysis of omics in-vitro studies. Dent Mater 2023; 39:101-113. [PMID: 36526446 DOI: 10.1016/j.dental.2022.11.022] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Since peri-implantitis differs clinically and histopathologically from periodontitis, implant wear debris is considered to play a role in the destructive processes. This work aims to systematically review if titanium particles affect oral-related cells through changes in molecular signatures (e.g., transcriptome, proteome, epigenome), thereby promoting peri-implantitis. METHODS Leveraging three literature databases (Medline, Embase, Cochrane) a systematic search based on a priori defined PICOs was conducted: '-omics' studies examining titanium exposure in oral-related cells. After risk of bias assessments, lists of differentially expressed genes, proteins, and results of functional enrichment analyses were compiled. The significance of overlapping genes across multiple studies was assessed via Monte Carlo simulation and their ranking was verified using rank aggregation. RESULTS Out of 2104 screened articles we found 12 eligible publications. A significant overlap of gene expression in oral-related cells exposed to titanium particles was found in four studies. Furthermore, changes in biological processes like immune/inflammatory or stress response as well as toll-like receptor (TLR) and mitogen-activated protein kinase (MAPK) signaling pathways were linked to titanium in transcriptome and proteome studies. Epigenetic changes caused by titanium were detected but inconsistent. CONCLUSION An influence of titanium implant wear debris on the development and progression of peri-implantitis is plausible but needs to be proven in further studies. Limitations arise from small sample sizes of included studies and insufficient publication of re-analyzable data.
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Affiliation(s)
- Lena Freitag
- Department of Conservative Dentistry and Periodontology, University Hospital, Ludwig-Maximilians-University, Goethestr. 70, D-80336 Munich, Germany
| | - Thomas Spinell
- Department of Conservative Dentistry and Periodontology, University Hospital, Ludwig-Maximilians-University, Goethestr. 70, D-80336 Munich, Germany.
| | - Annika Kröger
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK; Birmingham Community Healthcare NHS Foundation Trust, Birmingham, UK
| | | | - Michael Lauseker
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Reinhard Hickel
- Department of Conservative Dentistry and Periodontology, University Hospital, Ludwig-Maximilians-University, Goethestr. 70, D-80336 Munich, Germany
| | - Moritz Kebschull
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK; Birmingham Community Healthcare NHS Foundation Trust, Birmingham, UK; Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, Columbia University College of Dental Medicine, New York, NY, USA
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Hu X, Bai J, Liu R, Lv A. Comprehensive transcriptomics and proteomics analysis of Carassius auratus gills in response to Aeromonas hydrophila. Fish Shellfish Immunol Rep 2023; 4:100077. [PMID: 36589261 DOI: 10.1016/j.fsirep.2022.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
As one of the mucosal barriers, fish gills represent the first line of defense against pathogen infection. However, the exact mechanism of gill mucosal immune response to bacterial infection still needs further investigation in fish. Here, to investigate pathological changes and molecular mechanisms of the mucosal immune response in the gills of crucian carp (Carassius auratus) challenged by Aeromonas hydrophila, the transcriptomics and proteomics were performed by using multi-omics analyses of RNA-seq coupled with iTRAQ techniques. The results demonstrated gill immune response were mostly related to the activation of complement and coagulation cascades, antigen processing and presentation, phagosome, NOD-like receptor (NLR) and nuclear factor κB (NFκB) signaling pathway. Selected 21 immune-related DEGs (ie., Clam, nfyal, snrpf, acin1b, psme, sf3b5, rbm8a, rbm25, prpf18, g3bp2, snrpd3l, tecrem-2, cfl-A, C7, lysC, ddx5, hsp90, α-2M, C9, C3 and slc4a1a) were verified for their immune roles in the A. hydrophila infection via using qRT-PCR assay. Meanwhile, some complement (C3, C7, C9, CFD, DF and FH) and antigen presenting (HSP90, MHC Ⅱ, CALR, CANX and PSME) proteins were significantly participated in the process of defense against infections in gill tissues, and protein-protein interaction (PPI) network displayed the immune signaling pathways and interactions among these DEPs. The correlation analysis indicated that the iTRAQ and qRT-PCR results was significantly correlated (Pearson's correlation coefficient = 0.70, p < 0.01). To our knowledge, the transcriptomics and proteomics of gills firstly identified by multi-omics analyses contribute to understanding on the molecular mechanisms of local mucosal immunity in cyprinid species.
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Mohanta TK, Mohanta YK, Al-Harrasi A. Decoding the Virtual 2D Map of the Chloroplast Proteomes. Biol Proced Online 2022; 24:23. [PMID: 36513972 DOI: 10.1186/s12575-022-00186-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The chloroplast is a semi-autonomous organelle having its own genome and corresponding proteome. Although chloroplast genomes have been reported, no reports exist on their corresponding proteomes. Therefore, a proteome-wide analysis of the chloroplast proteomes of 2893 species was conducted, and a virtual 2D map was constructed. RESULTS The resulting virtual 2D map of the chloroplast proteome exhibited a bimodal distribution. The molecular mass of the chloroplast proteome ranged from 0.448 to 616.334 kDa, and the isoelectric point (pI) ranged from 2.854 to 12.954. Chloroplast proteomes were dominated by basic pI proteins with an average pI of 7.852. The molecular weight and isoelectric point of chloroplast proteome were found to show bimodal distribution. Leu was the most abundant and Cys the least abundant amino acid in the chloroplast proteome. Notably, Trp amino acid was absent in the chloroplast protein sequences of Pilostyles aethiopica. In addition, Selenocysteine (Sec) and Pyrrolysine (Pyl) amino acids were also found to be lacking in the chloroplast proteomes. CONCLUSION The virtual 2D map and amino acid composition of chloroplast proteome will enable the researchers to understand the biochemistry of chloroplast protein in detail. Further, the amino acid composition of the chloroplast proteome will also allow us to understand the codon usage bias. The codon usage bias and amino acid usage bias of chloroplast will be crucial to understanding their relationship.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Yugal Kishore Mohanta
- Department of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya, 793101, Techno City, India
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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He S, Klevebro S, Baldanzi G, Pershagen G, Lundberg B, Eneroth K, Hedman AM, Andolf E, Almqvist C, Bottai M, Melén E, Gruzieva O. Ambient air pollution and inflammation-related proteins during early childhood. Environ Res 2022; 215:114364. [PMID: 36126692 DOI: 10.1016/j.envres.2022.114364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIM Experimental studies show that short-term exposure to air pollution may alter cytokine concentrations. There is, however, a lack of epidemiological studies evaluating the association between long-term air pollution exposure and inflammation-related proteins in young children. Our objective was to examine whether air pollution exposure is associated with inflammation-related proteins during the first 2 years of life. METHODS In a pooled analysis of two birth cohorts from Stockholm County (n = 158), plasma levels of 92 systemic inflammation-related proteins were measured by Olink Proseek Multiplex Inflammation panel at 6 months, 1 year and 2 years of age. Time-weighted average exposure to particles with an aerodynamic diameter of <10 μm (PM10), <2.5 μm (PM2.5), and nitrogen dioxide (NO2) at residential addresses from birth and onwards was estimated via validated dispersion models. Stratified by sex, longitudinal cross-referenced mixed effect models were applied to estimate the overall effect of preceding air pollution exposure on combined protein levels, "inflammatory proteome", over the first 2 years of life, followed by cross-sectional protein-specific bootstrapped quantile regression analysis. RESULTS We identified significant longitudinal associations of inflammatory proteome during the first 2 years of life with preceding PM2.5 exposure, while consistent associations with PM10 and NO2 across ages were only observed among girls. Subsequent protein-specific analyses revealed significant associations of PM10 exposure with an increase in IFN-gamma and IL-12B in boys, and a decrease in IL-8 in girls at different percentiles of proteins levels, at age 6 months. Several inflammation-related proteins were also significantly associated with preceding PM10, PM2.5 and NO2 exposures, at ages 1 and 2 years, in a sex-specific manner. CONCLUSIONS Ambient air pollution exposure influences inflammation-related protein levels already during early childhood. Our results also suggest age- and sex-specific differences in the impact of air pollution on children's inflammatory profiles.
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Affiliation(s)
- Shizhen He
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Susanna Klevebro
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Gabriel Baldanzi
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Björn Lundberg
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Kristina Eneroth
- Environment and Health Administration, SLB-analys, Stockholm, Sweden
| | - Anna M Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ellika Andolf
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Matteo Bottai
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
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Blanco S, Morán P, Diz AP, Olabarria C, Vázquez E. Effects of short-term hyposalinity stress on four commercially important bivalves: A proteomic perspective. Environ Res 2022; 215:114371. [PMID: 36162473 DOI: 10.1016/j.envres.2022.114371] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/29/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Increased heavy rainfall can reduce salinity to values close to 0 in estuaries. Lethal and sublethal physiological and behavioural effects of decreases in salinity below ten have already been found to occur in the commercially important clam species Venerupis corrugata, Ruditapes decussatus and R. philippinarum and the cockle Cerastoderma edule, which generate an income of ∼74 million euros annually in Galicia (NW Spain). However, studies of the molecular response to hyposaline stress in bivalves are scarce. This 'shotgun' proteomics study evaluates changes in mantle-edge proteins subjected to short-term hyposaline episodes in two different months (March and May) during the gametogenic cycle. We found evidence that the mantle-edge proteome was more responsive to sampling time than to hyposalinity, strongly suggesting that reproductive stages condition the stress response. However, hyposalinity modulated proteome profiles in V. corrugata and C. edule in both months and R. philippinarum in May, involving proteins implicated in protein folding, redox homeostasis, detoxification, cytoskeleton modulation and the regulation of apoptotic, autophagic and lipid degradation pathways. However, proteins that are essential for an optimal osmotic stress response but which are highly energy demanding, such as chaperones, osmoprotectants and DNA repair factors, were found in small relative abundances. In both months in R. decussatus and in March in R. philippinarum, almost no differences between treatments were detected. Concordant trends in the relative abundance of stress response candidate proteins were also obtained in V. corrugata and C. edule in the different months, but not in Ruditapes spp., strongly suggesting that the osmotic stress response in bivalves is complex and possibly influenced by a combination of controlled (sampling time) and uncontrolled variables. In this paper, we report potential molecular targets for studying the response to osmotic stress, especially in the most osmosensitive native species C. edule and V. corrugata, and suggest factors to consider when searching for biomarkers of hyposaline stress in bivalves.
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Affiliation(s)
- S Blanco
- CIM - Centro de Investigación Mariña and Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, 36310, Vigo, Spain.
| | - P Morán
- CIM - Centro de Investigación Mariña and Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, 36310, Vigo, Spain
| | - A P Diz
- CIM - Centro de Investigación Mariña and Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, 36310, Vigo, Spain
| | - C Olabarria
- CIM - Centro de Investigación Mariña and Departamento de Ecoloxía e Bioloxía Animal, Facultade de Ciencias do Mar, Universidade de Vigo, 36310, Vigo, Spain
| | - E Vázquez
- CIM - Centro de Investigación Mariña and Departamento de Ecoloxía e Bioloxía Animal, Facultade de Ciencias do Mar, Universidade de Vigo, 36310, Vigo, Spain
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Shimizu K, Negishi L, Ito T, Touma S, Matsumoto T, Awaji M, Kurumizaka H, Yoshitake K, Kinoshita S, Asakawa S, Suzuki M. Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata. Comp Biochem Physiol Part D Genomics Proteomics 2022; 44:101025. [PMID: 36075178 DOI: 10.1016/j.cbd.2022.101025] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 01/27/2023]
Abstract
The molluscan shell is a good model for understanding the mechanisms underlying biomineralization. It is composed of calcium carbonate crystals and many types of organic molecules, such as the matrix proteins, polysaccharides, and lipids. The pen shell Atrina pectinata (Pterioida, Pinnidae) has two shell microstructures: an outer prismatic layer and an inner nacreous layer. Similar microstructures are well known in pearl oysters (Pteriidae), such as Pinctada fucata, and many kinds of shell matrix proteins (SMPs) have been identified from their shells. However, the members of SMPs that consist of the nacreous and prismatic layers of Pinnidae bivalves remain unclear. In this study, we identified 114 SMPs in the nacreous and prismatic layers of A. pectinata, of which only seven were found in both microstructures. 54 of them were found to bind calcium carbonate. Comparative analysis of nine molluscan shell proteomes showed that 69 of 114 SMPs of A. pectinata were found to have sequential similarity with at least one or more SMPs of other molluscan species. For instance, nacrein, tyrosinase, Pif/BMSP-like, chitinase (CN), chitin-binding proteins, CD109, and Kunitz-type serine proteinase inhibitors are widely shared among bivalves and gastropods. Our results provide new insights for understanding the complex evolution of SMPs related to nacreous and prismatic layer formation in the pteriomorph bivalves.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Takumi Ito
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shogo Touma
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Toshie Matsumoto
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie 516-0193, Japan
| | - Masahiko Awaji
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie 516-0193, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
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Lundquist H, Andersson H, Chew MS, Das J, Turkina MV, Welin A. The Olfactomedin-4-Defined Human Neutrophil Subsets Differ in Proteomic Profile in Healthy Individuals and Patients with Septic Shock. J Innate Immun 2022; 15:351-364. [PMID: 36450268 PMCID: PMC10701106 DOI: 10.1159/000527649] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/17/2022] [Indexed: 12/26/2023] Open
Abstract
The specific granule glycoprotein olfactomedin-4 (Olfm4) marks a subset (1-70%) of human neutrophils and the Olfm4-high (Olfm4-H) proportion has been found to correlate with septic shock severity. The aim of this study was to decipher proteomic differences between the subsets in healthy individuals, hypothesizing that Olfm4-H neutrophils have a proteomic profile distinct from that of Olfm4 low (Olfm4-L) neutrophils. We then extended the investigation to septic shock. A novel protocol for the preparation of fixed, antibody-stained, and sorted neutrophils for LC-MS/MS was developed. In healthy individuals, 39 proteins showed increased abundance in Olfm4-H, including the small GTPases Rab3d and Rab11a. In Olfm4-L, 52 proteins including neutrophil defensin alpha 4, CXCR1, Rab3a, and S100-A7 were more abundant. The data suggest differences in important neutrophil proteins that might impact immunological processes. However, in vitro experiments revealed no apparent difference in the ability to control bacteria nor produce oxygen radicals. In subsets isolated from patients with septic shock, 24 proteins including cytochrome b-245 chaperone 1 had significantly higher abundance in Olfm4-H and 30 in Olfm4-L, including Fc receptor proteins. There was no correlation between Olfm4-H proportion and septic shock severity, but plasma Olfm4 concentration was elevated in septic shock. Thus, the Olfm4-H and Olfm4-L neutrophils have different proteomic profiles, but there was no evident functional significance of the differences in septic shock.
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Affiliation(s)
- Hans Lundquist
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Henrik Andersson
- Department of Anaesthesia and Intensive Care, Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Michelle S Chew
- Department of Anaesthesia and Intensive Care, Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Jyotirmoy Das
- Bioinformatics, Core Facility, Division of Cell Biology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Clinical Genomics Linköping, SciLife Laboratory, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Maria V Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Amanda Welin
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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Le-Trilling VTK, Mennerich D, Schuler C, Sakson R, Lill JK, Kasarla SS, Kopczynski D, Loroch S, Flores-Martinez Y, Katschinski B, Wohlgemuth K, Gunzer M, Meyer F, Phapale P, Dittmer U, Sickmann A, Trilling M. Identification of herbal teas and their compounds eliciting antiviral activity against SARS-CoV-2 in vitro. BMC Biol 2022; 20:264. [PMID: 36447206 PMCID: PMC9708519 DOI: 10.1186/s12915-022-01468-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The SARS-CoV-2/COVID-19 pandemic has inflicted medical and socioeconomic havoc, and despite the current availability of vaccines and broad implementation of vaccination programs, more easily accessible and cost-effective acute treatment options preventing morbidity and mortality are urgently needed. Herbal teas have historically and recurrently been applied as self-medication for prophylaxis, therapy, and symptom alleviation in diverse diseases, including those caused by respiratory viruses, and have provided sources of natural products as basis for the development of therapeutic agents. To identify affordable, ubiquitously available, and effective treatments, we tested herbs consumed worldwide as herbal teas regarding their antiviral activity against SARS-CoV-2. RESULTS Aqueous infusions prepared by boiling leaves of the Lamiaceae perilla and sage elicit potent and sustained antiviral activity against SARS-CoV-2 when applied after infection as well as prior to infection of cells. The herbal infusions exerted in vitro antiviral effects comparable to interferon-β and remdesivir but outperformed convalescent sera and interferon-α2 upon short-term treatment early after infection. Based on protein fractionation analyses, we identified caffeic acid, perilla aldehyde, and perillyl alcohol as antiviral compounds. Global mass spectrometry (MS) analyses performed comparatively in two different cell culture infection models revealed changes of the proteome upon treatment with herbal infusions and provided insights into the mode of action. As inferred by the MS data, induction of heme oxygenase 1 (HMOX-1) was confirmed as effector mechanism by the antiviral activity of the HMOX-1-inducing compounds sulforaphane and fraxetin. CONCLUSIONS In conclusion, herbal teas based on perilla and sage exhibit antiviral activity against SARS-CoV-2 including variants of concern such as Alpha, Beta, Delta, and Omicron, and we identified HMOX-1 as potential therapeutic target. Given that perilla and sage have been suggested as treatment options for various diseases, our dataset may constitute a valuable resource also for future research beyond virology.
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Affiliation(s)
- Vu Thuy Khanh Le-Trilling
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Denise Mennerich
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Corinna Schuler
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Roman Sakson
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany
| | - Julia K. Lill
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany
| | - Siva Swapna Kasarla
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany
| | - Dominik Kopczynski
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany
| | - Stefan Loroch
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany
| | - Yulia Flores-Martinez
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Benjamin Katschinski
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Kerstin Wohlgemuth
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Matthias Gunzer
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany ,grid.5718.b0000 0001 2187 5445Institute for Experimental Immunology and Imaging, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Folker Meyer
- grid.5718.b0000 0001 2187 5445Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Prasad Phapale
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany
| | - Ulf Dittmer
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
| | - Albert Sickmann
- grid.419243.90000 0004 0492 9407Leibniz-Institut Für Analytische Wissenschaften - ISAS - E.V., Dortmund, Germany ,grid.5570.70000 0004 0490 981XMedizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany ,grid.7107.10000 0004 1936 7291Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
| | - Mirko Trilling
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 179, 45147 Essen, Germany
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Stransky S, Cutler R, Aguilan J, Nieves E, Sidoli S. Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model. Epigenetics Chromatin 2022; 15:35. [PMID: 36411440 PMCID: PMC9677638 DOI: 10.1186/s13072-022-00470-7] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Three-dimensional (3D) cell culture has emerged as an alternative approach to 2D flat culture to model more accurately the phenotype of solid tissue in laboratories. Culturing cells in 3D more precisely recapitulates physiological conditions of tissues, as these cells reduce activities related to proliferation, focusing their energy consumption toward metabolism and homeostasis. RESULTS Here, we demonstrate that 3D liver spheroids are a suitable system to model chromatin dynamics and response to epigenetics inhibitors. To delay necrotic tissue formation despite proliferation arrest, we utilize rotating bioreactors that apply active media diffusion and low shearing forces. We demonstrate that the proteome and the metabolome of our model resemble typical liver functions. We prove that spheroids respond to sodium butyrate (NaBut) treatment, an inhibitor of histone deacetylases (HDACi), by upregulating histone acetylation and transcriptional activation. As expected, NaBut treatment impaired specific cellular functions, including the energy metabolism. More importantly, we demonstrate that spheroids reestablish their original proteome and transcriptome, including pre-treatment levels of histone acetylation, metabolism, and protein expression once the standard culture condition is restored after treatment. Given the slow replication rate (> 40 days) of cells in 3D spheroids, our model enables to monitor the recovery of approximately the same cells that underwent treatment, demonstrating that NaBut does not have long-lasting effects on histone acetylation and gene expression. These results suggest that our model system can be used to quantify molecular memory on chromatin. CONCLUSION Together, we established an innovative cell culture system that can be used to model anomalously decondensing chromatin in physiological cell growth and rule out epigenetics inheritance if cells recover the original phenotype after treatment. The transient epigenetics effects demonstrated here highlight the relevance of using a 3D culture model system that could be very useful in studies requiring long-term drug treatment conditions that would not be possible using a 2D cell monolayer system.
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Affiliation(s)
- Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Ronald Cutler
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA.,Department of Genetics, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Jennifer Aguilan
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA.,Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA.
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do Nascimento NC, Bailey TW, Santos AP, Duan C, Mohallem R, Franco J, Aryal UK, Xie J, Cox A, Sivasankar MP. Proteomic analysis reveals that aging rabbit vocal folds are more vulnerable to changes caused by systemic dehydration. BMC Genomics 2022; 23:762. [PMID: 36411412 PMCID: PMC9677652 DOI: 10.1186/s12864-022-08975-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Older adults are more prone to develop systemic dehydration. Systemic dehydration has implications for vocal fold biology by affecting gene and protein expression. The objective of this study was to quantify vocal fold protein changes between two age groups and hydration status, and to investigate the interaction of age and hydration status on protein expression, which has not been investigated in the context of vocal folds before. Comparative proteomics was used to analyze the vocal fold proteome of 6.5-month-old and > 3-year-old rabbits subjected to water ad libitum or water volume restriction protocol. RESULTS Young and older adult rabbits (n = 22) were either euhydrated (water ad libitum) or dehydrated by water volume restriction. Dehydration was confirmed by body weight loss of - 5.4% and - 4.6% in young and older groups, respectively, and a 1.7-fold increase of kidney renin gene expression in the young rabbits. LC-MS/MS identified 2286 proteins in the rabbit vocal folds of young and older adult rabbits combined. Of these, 177, 169, and 81 proteins were significantly (p ≤ 0.05) affected by age, hydration status, or the interaction of both factors, respectively. Analysis of the interaction effect revealed 32 proteins with opposite change patterns after dehydration between older and young rabbit vocal folds, while 31 proteins were differentially regulated only in the older adult rabbits and ten only in the young rabbits in response to systemic dehydration. The magnitude of changes for either up or downregulated proteins was higher in the older rabbits. These proteins are predominantly related to structural components of the extracellular matrix and muscle layer, suggesting a disturbance in the viscoelastic properties of aging vocal fold tissue, especially when subjected to systemic dehydration. CONCLUSIONS Water restriction is a laboratory protocol to assess systemic dehydration-related changes in the vocal fold tissue that is translatable to human subjects. Our findings showed a higher number of proteins differentially regulated with a greater magnitude of change in the vocal folds of older adult rabbits in the presence of systemic dehydration compared to younger rabbits. The association of these proteins with vocal fold structure and biomechanical properties suggests that older human subjects may be more vulnerable to the effects of systemic dehydration on vocal function. The clinical implications of these protein changes warrant more investigation, but age should be taken into consideration when evaluating vocal treatment recommendations that interfere with body fluid balance.
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Affiliation(s)
- Naila C. do Nascimento
- grid.169077.e0000 0004 1937 2197Department of Speech, Language, and Hearing Sciences, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Taylor W. Bailey
- grid.169077.e0000 0004 1937 2197Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Andrea P. Santos
- grid.169077.e0000 0004 1937 2197Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Chenwei Duan
- grid.169077.e0000 0004 1937 2197Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Rodrigo Mohallem
- grid.169077.e0000 0004 1937 2197Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Proteomics Facility, Bindley Bioscience Center, Discovery Park, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Jackeline Franco
- grid.169077.e0000 0004 1937 2197Purdue Proteomics Facility, Bindley Bioscience Center, Discovery Park, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Uma K. Aryal
- grid.169077.e0000 0004 1937 2197Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Proteomics Facility, Bindley Bioscience Center, Discovery Park, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Jun Xie
- grid.169077.e0000 0004 1937 2197Department of Statistics, Purdue University, West Lafayette, Indiana, 47907 USA
| | - Abigail Cox
- grid.169077.e0000 0004 1937 2197Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, 47907 USA
| | - M. Preeti Sivasankar
- grid.169077.e0000 0004 1937 2197Department of Speech, Language, and Hearing Sciences, Purdue University, West Lafayette, Indiana, 47907 USA
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174
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Mindikoglu AL, Park J, Opekun AR, Abdulsada MM, Wilhelm ZR, Jalal PK, Devaraj S, Jung SY. Dawn-to-dusk dry fasting induces anti-atherosclerotic, anti-inflammatory, and anti-tumorigenic proteome in peripheral blood mononuclear cells in subjects with metabolic syndrome. Metabol Open 2022; 16:100214. [PMID: 36506940 PMCID: PMC9731888 DOI: 10.1016/j.metop.2022.100214] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background Metabolic syndrome characterized by abdominal obesity, high blood pressure, elevated fasting glucose and triglyceride levels and low high-density lipoprotein cholesterol level is associated with pro-inflammatory state, increased risk for atherosclerosis, and multiple cancers. Our previous results on subjects with metabolic syndrome showed that 4-week dawn-to-dusk (sunset) dry fasting resulted in significant changes in the serum proteome and improvement in several metabolic risk factors. Peripheral blood mononuclear cells (PBMC) proteomics is a powerful tool that can provide mechanistic insights into how dawn-to-dusk dry fasting affects protein expression in metabolic pathways at cellular level. In this study, we determined whether dawn-to-dusk dry fasting would induce favorable changes in PBMC proteome in subjects with metabolic syndrome, similar to the changes induced by dawn-to-dusk dry fasting in the same subjects' serum proteome. Methods We conducted a prospective study on subjects with metabolic syndrome and collected blood specimens before 4-week dawn-to-dusk dry fasting, at the end of 4-week dawn-to-dusk dry fasting, and one week after 4-week dawn-to-dusk dry fasting. We performed untargeted proteomics using nano ultra-high performance liquid chromatography-tandem mass spectrometry to assess the impact of 4-week dawn-to-dusk dry fasting on PBMC proteome. Results There were 14 subjects with metabolic syndrome with a mean age of 59 who fasted from dawn to dusk (strict dry fasting without any liquid or food intake) for more than 14 h daily for 29 days. The quantitative proteome analysis showed that apolipoprotein B (APOB) gene protein products (GP) levels were downregulated and had the most statistical significance of the observed difference at the end of 4-week dawn-to-dusk dry fasting (P = 0.008) and one week after 4-week dawn-to-dusk dry fasting (P = 0.0004) compared with the levels before 4-week dawn-to-dusk dry fasting. The comparison between GP levels before and at the end of 4-week dawn-to-dusk dry fasting showed an alteration in the expression of genes associated with lipid and atherosclerosis pathway (P = 6.014e-4) and C-type lectin receptor signaling pathway (P = 1.064e-5). The genes that were differentially expressed in the lipid and atherosclerosis pathway were APOB (P = 0.008), CD36 (P = 0.040), CALM1, CALM2, CALM3 (P = 0.015), and HSPA8 (P = 0.047). One of the differentially expressed genes in the C-type lectin receptor signaling pathway was lymphocyte-specific protein 1 (LSP1), which showed an average of 19-fold increase at the end of 4-week dawn-to-dusk dry fasting compared with the GP levels before fasting (P = 0.004). Several GPs associated with tumor-suppressor effect (TUBB4B, LSP1, ACTR3B) were upregulated, and GPs associated with tumor-promoter effect (CD36, CALM1, CALM2, CALM3, FLOT2, PPIF) were downregulated at the end of 4-week dawn-to-dusk dry fasting or one week after 4-week dawn-to-dusk dry fasting compared with the GP levels before 4-week dawn-to-dusk dry fasting. Conclusion Based on our results, we conclude that in subjects with metabolic syndrome, 4-week dawn-to-dusk dry fasting induced anti-atherosclerotic, anti-inflammatory, and anti-tumorigenic PMBC proteome. Randomized, controlled clinical trials are needed to further investigate the effect of dawn-to-dusk dry fasting on subjects with chronic metabolic diseases and metabolic syndrome-induced cancers.
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Affiliation(s)
- Ayse L. Mindikoglu
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA,Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation, Baylor College of Medicine, Houston, TX, USA,Corresponding author. Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA.
| | - Jihwan Park
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Antone R. Opekun
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA,Department of Pediatrics, Division of Gastroenterology, Nutrition and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Mustafa M. Abdulsada
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Zoe R. Wilhelm
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Prasun K. Jalal
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA,Michael E. DeBakey Department of Surgery, Division of Abdominal Transplantation, Baylor College of Medicine, Houston, TX, USA
| | - Sridevi Devaraj
- Clinical Chemistry and Point of Care Technology, Texas Children's Hospital, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Sung Yun Jung
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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He S, Zhou X, Yang G, Zhou Z, Zhang Y, Shao X, Liang T, Lv N, Chen J, Qian Z. Proteomic comparison between physiological degeneration and needle puncture model of disc generation disease. Eur Spine J 2022; 31:2920-2934. [PMID: 35842490 DOI: 10.1007/s00586-022-07284-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/20/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The completeness of the intervertebral disc proteome is fundamental to the integrity and functionality of the intervertebral disc. METHODS The 20 experimental rats were placed into two groups randomly, normal group (NG) and acupuncture pathological degeneration group-2 weeks (APDG-2w). The ten 24-month-old rats were grouped into physiological degeneration group (PDG). Magnetic resonance imaging, X-ray examination, histological staining (hematoxylin & eosin, safranin-O cartilage, and alcian blue staining), and immunohistochemical examination were carried out for assessing the degree of disc degradation. Intervertebral disc was collected, and protein composition was determined by LC- MS, followed by bioinformatic analysis including significance analysis, subcellular localization prediction, protein domain prediction, GO function and KEGG pathway analysis, and protein interaction network construction. LC-PRM was done for protein quantification. RESULTS Physiological degeneration and especially needle puncture decreased T2 signal intensity and intervertebral disc height. Results from hematoxylin & eosin, safranin-O, and alcian blue staining revealed that the annulus fibrosus apparently showed the wavy and collapsed fibrocartilage lamellas in APDG-2w and PDG groups. The contents of the nucleus pulposus were decreased in physiological degeneration group and APDG-2w group compared with NG. Results from immunohistochemical analysis suggested the degeneration of intervertebral disc and inflammation in APDG-2w and PDG groups. The protein composition and expression between needle puncture rat models and the physiological degeneration group showed significant difference. CONCLUSIONS Our studies produced point-reference datasets of normal rats, physiological degeneration rats, and needle puncture rat models, which is beneficial to subsequent pathological studies. There is differential expression of protein expression in degenerative discs with aging and acupuncture, which may be used as a potential discriminating index for different intervertebral degenerations.
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Affiliation(s)
- Shuangjun He
- Department of Orthopedic Surgery, Affiliated Danyang Hospital of Nantong University, The People's Hospital of Danyang, Xinmin Road 2, Danyang, Zhenjiang, 212300, Jiangsu, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China
| | - Xinfeng Zhou
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China
| | - Guotao Yang
- Department of Orthopedic Surgery, Affiliated Danyang Hospital of Nantong University, The People's Hospital of Danyang, Xinmin Road 2, Danyang, Zhenjiang, 212300, Jiangsu, China
| | - Zhangzhe Zhou
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China
| | - Yijian Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China
| | - Xiaofeng Shao
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China
| | - Ting Liang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China
| | - Nanning Lv
- Department of Orthopedic Surgery, The Second People's Hospital of Lianyungang, 41 Hailian Street, Lianyungang, Jiangsu, China.
| | - Jianhong Chen
- Department of Orthopedic Surgery, Affiliated Danyang Hospital of Nantong University, The People's Hospital of Danyang, Xinmin Road 2, Danyang, Zhenjiang, 212300, Jiangsu, China.
| | - Zhonglai Qian
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu, China.
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Pamei I, Makandar R. Comparative proteome analysis reveals the role of negative floral regulators and defense-related genes in phytoplasma infected sesame. Protoplasma 2022; 259:1441-1453. [PMID: 35190871 DOI: 10.1007/s00709-022-01737-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
"Candidatus Phytoplasma australiense" is associated with floral malformations in sesame but the interaction remains largely unexplored. A label-free quantitative shotgun proteomics approach through liquid chromatography-mass spectrometry quadruple time-of-flight was used to analyze changes in the proteome of asymptomatic (control) and symptomatic (phytoplasma-infected) sesame plants to identify proteins differentially expressed during phytoplasma infection at early stages of flower development. A total of 3457 and 1704 proteins were identified from asymptomatic and symptomatic samples respectively through proteome profiling with three runs per sample. Several differentially abundant proteins (DAPs) were identified which might be involved in sesame-phytoplasma interaction. The DAPs identified were related to transcription, cell division, chromosome partitioning, defense mechanisms, negative regulation of flower development, amino acid transport and metabolism, signal transduction and RNA processing, and its modifications. Of these proteins, 21 were downregulated while 212 were significantly upregulated in symptomatic sesame plants compared to the control plants. The floral development-related proteins like UBP16 and DCAF1 were found to be downregulated while negative regulators/repressors of floral development genes, HUA2, PIE1, and ICU2, were upregulated in symptomatic samples indicating phytoplasma's role in altering the expression of these genes. Validation of these genes through quantitative retro-transcripted PCR suggested that the DAPs observed in symptomatic sesame might be induced by phytoplasma presence to suppress flowering via negative regulation of flower development.
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Affiliation(s)
- Injangbuanang Pamei
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Ragiba Makandar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad, 500046, India.
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Xiang QQ, Kang YH, Lian LH, Chen ZY, Wang P, Hu JM, Chen LQ. Proteomic profiling reveals mitochondrial toxicity of nanosilver and silver nitrate in the gill of common carp. Aquat Toxicol 2022; 252:106318. [PMID: 36206702 DOI: 10.1016/j.aquatox.2022.106318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 08/31/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Mitochondria are recognized as an important target organelle for the toxicity of nanomaterials. Although the toxic effects of silver nanoparticles (AgNPs) on mitochondria have been widely reported, the mechanism behind the toxicity remains unclear. In this study, the effects of two forms of silver (AgNPs and AgNO3) on carp gill mitochondria were investigated by analyzing the mitochondrial ultrastructure, physicochemical properties of mitochondrial membrane, and mitochondrial proteomics. After exposure of common carp to AgNPs (0.75 mg/L) and AgNO3 (0.05 mg/L) for 96 h, both forms of silver were shown to cause gill mitochondrial lesions, including irregular shape, loss of mitochondrial cristae, and increased mitochondrial membrane permeability. Proteomics results revealed that AgNPs and AgNO3 induced 362 and 297 differentially expressed proteins (DEPs) in gill mitochondria, respectively. Among the DEPs, 244 were shared between AgNPs and AgNO3 treatments. These shared proteins were mainly distributed in the mitochondrial membrane and matrix, and were significantly enriched in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation pathway. The functional annotation of DEPs induced by both silver forms was mainly involved in energy production and conversion. These results indicated that the toxic mechanism of AgNPs and AgNO3 on gill mitochondria were comparable and the two forms of silver caused mitochondrial dysfunction in fish gills by inhibiting the TCA cycle and disrupting the electron transport chain.
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Affiliation(s)
- Qian-Qian Xiang
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming 650091, PR China
| | - Yu-Hang Kang
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming 650091, PR China
| | - Li-Hong Lian
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming 650091, PR China
| | - Zhi-Ying Chen
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming 650091, PR China
| | - Peng Wang
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, PR China
| | - Jin-Ming Hu
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming 650091, PR China
| | - Li-Qiang Chen
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming 650091, PR China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming 650091, PR China.
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178
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Klodová B, Potěšil D, Steinbachová L, Michailidis C, Lindner AC, Hackenberg D, Becker JD, Zdráhal Z, Twell D, Honys D. Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. Plant Reprod 2022:10.1007/s00497-022-00452-5. [PMID: 36282332 PMCID: PMC10363097 DOI: 10.1007/s00497-022-00452-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronized gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.
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Affiliation(s)
- Božena Klodová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Praha 2, 128 00, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ann-Cathrin Lindner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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Abstract
More and more it is being appreciated that not all GPCRs are the same, sub-populations of GPCRs exist within a cell and function differently than others. The question is, how does one regulate a given sub-population? One way is through the addition of post-translational modifications to G-protein coupled receptors (GPCR). This process has long been known to occur and play a role in trafficking, pharmacology and ultimately function. This chapter will focus on one particular modification, that of S-palmitoylation, and its impact on GPCR function. We will discuss the history of this modification on these receptors and the connection with disease. We will highlight several examples from the literature of where palmitoylation impacts GPCR function.
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Affiliation(s)
- Georges Chalhoub
- Department of Endocrinology, Queen Mary University of London, London, United Kingdom
| | - Peter J McCormick
- Department of Endocrinology, Queen Mary University of London, London, United Kingdom.
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180
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Yang X, Fu Z, Ren Q, Wang S, Yin S, Liu J. Correlation of synovial tissue protein abundance with menopause in osteoarthritis. Am J Transl Res 2022; 14:7403-7412. [PMID: 36398240 PMCID: PMC9641427] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Osteoarthritis (OA) is a common articular disorder. Epidemiologic surveys show a higher prevalence of OA in women than men and that morbidity is higher during menopause. We aimed to explore whether menopause influences the clinical recovery of a knee joint following OA and injury, and identify associated mechanisms by analyzing the proteomic profile of synovial tissue (ST) samples. METHODS Routine blood examination and hormone level tests were conducted before surgery. ST samples from eight participants were collected intraoperatively for proteomic analysis. One day before and one month after the surgery, we assessed various aspects of function in the affected knee including the with Visual Analog Score (VAS), Lysholm, The Western Ontario, and McMaster Universities Osteoarthritis Index (WOMAC) scores. The relationships between proteomic data, estrogen levels, and affected knee function were compared and analyzed. This was a retrospective study. RESULT Menopause was associated with the clinical outcomes of knee OA and knee injuries. ST proteomic data identified that 80 proteins in premenopausal OA females were significantly different from menopausal OA females. In addition, 100 proteins were significantly different between premenopausal OA females and premenopausal injured females. CONCLUSIONS Age and menopause showed a positive correlation with the protein profile of ST from OA or knee injury female patients, indicating that the protein components might be affected by menopause. Postoperative clinical outcomes were affected by menopause. We conclude that menopause may, in part, regulate knee joint function by altering ST protein expression.
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Affiliation(s)
- Xiao Yang
- Graduate School of Tianjin Medical UniversityTianjin, China
- Department of Orthopaedics, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s HospitalChengdu, Sichuan, China
| | - Zhe Fu
- Graduate School of Tianjin Medical UniversityTianjin, China
- Department of Orthopaedics, Tianjin Hospital, Tianjin UniversityTianjin, China
| | - Qiuyu Ren
- Department of Orthopaedics, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s HospitalChengdu, Sichuan, China
| | - Shuang Wang
- Department of Orthopaedics, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s HospitalChengdu, Sichuan, China
| | - Shuai Yin
- Graduate School of Tianjin Medical UniversityTianjin, China
- Department of Orthopaedics, Cangzhou Hospital of Integrated TCM-WMCangzhou, Hebei, China
| | - Jun Liu
- Graduate School of Tianjin Medical UniversityTianjin, China
- Department of Orthopaedics, Tianjin Hospital, Tianjin UniversityTianjin, China
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181
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Yuan J, Cheng L, Li H, An C, Wang Y, Zhang F. Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro. BMC Plant Biol 2022; 22:481. [PMID: 36210448 PMCID: PMC9549635 DOI: 10.1186/s12870-022-03852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. RESULTS A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. CONCLUSIONS This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.
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Affiliation(s)
- Jianlong Yuan
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lixiang Cheng
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huijun Li
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Congcong An
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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182
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Luo W, Wang J, Chen Y, Wang Y, Li R, Tang J, Geng F. Quantitative proteomic analysis provides insight into the survival mechanism of Salmonella typhimurium under high-intensity ultrasound treatment. Curr Res Food Sci 2022; 5:1740-1749. [PMID: 36268134 PMCID: PMC9576580 DOI: 10.1016/j.crfs.2022.09.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/21/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
The survival mechanism of Salmonella treated with high-intensity ultrasound (HIU) should be explored to further enhance the bactericidal efficacy of HIU. In this study, culturable Salmonella was reduced by applying HIU. Electron microscope imaging revealed that HIU caused the disintegration of cell structure and leakage of intracellular substances. For the Salmonella after the HIU treatment, key enzymes of the tricarboxylic acid [TCA] cycle were significantly downregulated, which led to a reduced ATP content (45.25%–75.00%), although ATPase activity was augmented by 33.82%–60.64% in the Salmonella. Accordingly, surviving Salmonella could have tolerated the stress of HIU by upregulating their environmental sensing (two-component system), chemotaxis (bacterial chemotaxis), substance uptake (ABC transporter), and ATP production (oxidative phosphorylation). Therefore, synergistically blocking the ATP production, signal transduction, or substance intake of Salmonella offer promising potential strategies to improve the bactericidal effect of HIU in industrial food processing. Cell damage and substances leakage were observed in ultrasound treated Salmonella. Ultrasonic treatments caused 1017 differentially expressed proteins in Salmonella. Ultrasound inhibited tricarboxylic acid cycle and reduced adenosine triphosphate content in Salmonella. Salmonella tolerated ultrasound by upregulating two-component system, ABC transport, and bacterial chemotaxis. These altered pathways could be potential targets to enhance the lethality of ultrasound.
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Affiliation(s)
- Wei Luo
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Jinqiu Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Yan Chen
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Yixu Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plants, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Jie Tang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Fang Geng
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China,Corresponding author.
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183
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Li Z, Bao H. Deciphering key regulators of Inonotus hispidus petroleum ether extract involved in anti-tumor through whole transcriptome and proteome analysis in H22 tumor-bearing mice model. J Ethnopharmacol 2022; 296:115468. [PMID: 35718054 DOI: 10.1016/j.jep.2022.115468] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The mushroom Inonotus hispidus is traditional Chinese medicine, which has been used to treat tumor illness for a long history in China. Our previous research found that I. hispidus petroleum ether extract (IPE) has significant anti-tumor activity. However, the potential anti-tumor regulatory pathways and targets of I. hispidus remain unclear. OBJECTIVE The present study was envisaged to explore the key regulators responsible for anti-tumor of IPE using whole transcriptome and proteome analysis in H22 tumor-bearing mice model. MATERIALS AND METHODS The model of H22 tumor-bearing mice was constructed according to the histopathological data and biochemical parameters. The isolated tumor tissues of different treatment groups were subjected to transcriptomic and proteomic analysis. An integrated approach of RNA-Seq, proteomics, and system biology analysis was used to identify key regulators involved in antitumor pathways. The analyzed differential expression patterns were supported by gene and protein expression studies. RESULTS These results indicated that 957 differentially expressed genes and 405 proteins were identified in the tumor tissue of different treatment groups through RNA-Seq and liquid chromatography with tandem mass spectrometry-based proteomic analysis, respectively. The combined omics analysis revealed five critical genes/proteins, including Lilrb4a, Nrp1, Gzma, Gstt1, and Pdk4 that could play a role in antitumor pathways. Furthermore, Lilrb4a, Nrp1, Gzma, Gstt1 and Pdk4 genes/proteins, as key regulators of the anti-tumor effect of IPE, were verified by qRT-PCR and western blotting methods, respectively. CONCLUSION Our study provides new ideas for analyzing the antitumor mechanism of IPE from the point of view of gene and protein expression and will encourage further development of the I. hispidus pharmaceutical industry.
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Affiliation(s)
- Zhijun Li
- Key Laboratory of Edible Fungi Resources and Utilization, Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, 130118, China; College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China.
| | - Haiying Bao
- Key Laboratory of Edible Fungi Resources and Utilization, Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, 130118, China; College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China.
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184
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Hu C, Li J, Liu M, Lam PKS, Chen L. Young fecal transplantation modulates the visual toxicity of perfluorobutanesulfonate in aged zebrafish recipients. Aquat Toxicol 2022; 251:106295. [PMID: 36103760 DOI: 10.1016/j.aquatox.2022.106295] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Perfluorobutanesulfonate (PFBS) is an emerging pollutant of potent toxicity to impair visual system. Previous studies highlighted the applicability of gut microbiota manipulation to mitigate the toxicities of PFBS. However, it remains unknown whether transplantation of whole fecal microbiota to PFBS-disturbed gut can restore the health of the recipient animals, especially for aged fish that are of high susceptibility. In the present study, aged zebrafish of 3 years old were first transplanted with feces from young counterparts and then exposed to environmentally relevant concentrations of PFBS. After exposure, toxic effects of PFBS on visual system of aged zebrafish were elucidated based on transcriptional, proteomic, biochemical, histological, and behavioral evidences. In addition, interaction between young fecal transplant and innate visual toxicity of PFBS was further explored in the aged. The results showed that PFBS singular exposure induced lipid peroxidation (by 1.9-fold) in aged male eyes, which were alleviated by young fecal transplantation. PFBS also disturbed the retinal structure of the aged, which was characterized by increases in plexiform layers, but decreases in ganglion neuron number (by 26.8% and 26.0% in males and females, respectively) and optic nerve width (by 14.1% and 12.7% in males and females, respectively). It was unexpected that young fecal transplant was very potent in re-organizing the histological assembly of aged eyes regardless of PFBS coexposure, underlining the intimate interplay between gut and retina. Proteomic profiling provided more clues about the visual toxicology mechanism of PFBS, which was found to typically interfere with synaptic neurotransmission occurring in plexiform layers. However, proteome perturbation of aged eyes by PFBS exposure was effectively shifted by the transplantation of young feces towards the control phenotype, suggesting the high ameliorative potential of young fecal transplantation along the gut-retina axis. Overall, the present study pinpoints the potent visual toxicity of PFBS in aged animals and highlights the efficacy of young fecal transplant to regulate the inherent toxicity of PFBS. Future studies are necessitated to sequence the gut microbiota and unveil the underlying interactive routes between gut microbes and visual system.
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Affiliation(s)
- Chenyan Hu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430072, China
| | - Jing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengyuan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Paul K S Lam
- Office of the President, Hong Kong Metropolitan University, 30 Good Shepherd Street, Kowloon, China Hong Kong Special Administrative Region
| | - Lianguo Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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185
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Savikj M, Stocks B, Sato S, Caidahl K, Krook A, Deshmukh AS, Zierath JR, Wallberg-Henriksson H. Exercise timing influences multi-tissue metabolome and skeletal muscle proteome profiles in type 2 diabetic patients - A randomized crossover trial. Metabolism 2022; 135:155268. [PMID: 35908579 DOI: 10.1016/j.metabol.2022.155268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/10/2022] [Accepted: 07/22/2022] [Indexed: 01/06/2023]
Abstract
AIMS/HYPOTHESIS Metabolic effects of exercise may partly depend on the time-of-day when exercise is performed. We tested the hypothesis that exercise timing affects the adaptations in multi-tissue metabolome and skeletal muscle proteome profiles in men with type 2 diabetes. METHODS Men fitting the inclusion (type 2 diabetes, age 45-68 years and body mass index 23-33 kg/m2) and exclusion criteria (insulin treatment, smoking, concurrent systemic disease, and regular exercise training) were included in a randomized crossover trial (n = 15). Participants included in this metabolomics and proteomics analysis fully completed all exercise sessions (n = 8). The trial consisted of two weeks of high-intensity interval training (HIT) (three sessions/week) either in the morning (08:00, n = 5) or afternoon (16:45, n = 3), a two-week wash-out period, and an additional two weeks of HIT at the opposing time. Participants and researchers were not blinded to group allocation. Blood, skeletal muscle and subcutaneous adipose tissue were obtained before the first, and after each training period. Broad-spectrum, untargeted proteomic analysis was performed on skeletal muscle, and metabolomic analysis was performed on all biosamples. Differential content was assessed by linear regression and pathway set enrichment analyses were performed. Coordinated metabolic changes across tissues were identified by Spearman correlation analysis. RESULTS Metabolic and proteomic profiles remained stable after two weeks of HIT, and individual metabolites and proteins were not altered, irrespective of the time of day at which the training was performed. However, coordinated changes in relevant metabolic pathways and protein categories were identified. Morning and afternoon HIT similarly increased plasma diacylglycerols, skeletal muscle acyl-carnitines, and subcutaneous adipose tissue sphingomyelins and lysophospholipids. Acyl-carnitines were central to training-induced metabolic cross-talk across tissues. Plasma carbohydrates, via the penthose phosphate pathway, were increased and skeletal muscle lipids were decreased after morning compared to afternoon HIT. Skeletal muscle lipoproteins were higher, and mitochondrial complex III abundance was lower after morning compared to afternoon HIT. CONCLUSIONS/INTERPRETATION We provide a comprehensive analysis of a multi-tissue metabolomic and skeletal muscle proteomic responses to training at different times of the day in men with type 2 diabetes. Increased circulating lipids and changes in adipose tissue lipid composition were common between morning and afternoon HIT. However, afternoon HIT increased skeletal muscle lipids and mitochondrial content to a greater degree than morning training. Thus, there is a diurnal component in the metabolomic and proteomic response to exercise in men with type 2 diabetes. The clinical relevance of this response warrants further investigation.
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Affiliation(s)
- Mladen Savikj
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ben Stocks
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shogo Sato
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kenneth Caidahl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Krook
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juleen R Zierath
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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186
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Chen L, Gu T, Wu T, Ding L, Ge Q, Zhang Y, Ma S. Proteotranscriptomic Integration analyses reveals new mechanistic insights regarding Bombyx mori fluorosis. Food Chem Toxicol 2022; 169:113414. [PMID: 36174832 DOI: 10.1016/j.fct.2022.113414] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/07/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022]
Abstract
The commercial value of silkworms has been widely explored and the effects of fluoride exposure on silkworms' breeding and silk production cannot be ignored. Bombyx mori is a commonly used model to explore the mechanisms of fluorosis. In the present study, we analyzed the differences in physiological and biochemical indicators after exposing larva to NaF, then evaluated differential genes and proteins. Compared to control, larvae exposed to 600 mg L-1 NaF presented decreased bodyweight, damaged midgut tissue, and were accompanied by oxidative stress. The RNA-seq showed 1493 differentially expressed genes (574 upregulated and 919 downregulated). Meanwhile, the TMT detected 189 differentially expressed proteins (133 upregulated and 56 downregulated). The integrative analysis led to 4 upregulated and 9 downregulated genes and proteins. Finally, we hypothesized that fluoride exposure might affect the intestinal digestion of silkworms, inhibit the gene expression of detoxification enzymes and stimulate cellular immune responses. Our current findings provided new insights into insect fluorosis.
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Affiliation(s)
- Liang Chen
- School of Life Sciences, Jiangsu University, 212013, Zhenjiang, China.
| | - Tongyu Gu
- School of Life Sciences, Jiangsu University, 212013, Zhenjiang, China
| | - Tong Wu
- School of Life Sciences, Jiangsu University, 212013, Zhenjiang, China
| | - Lei Ding
- School of Life Sciences, Jiangsu University, 212013, Zhenjiang, China
| | - Qi Ge
- School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, China
| | - Yao Zhang
- School of Life Sciences, Jiangsu University, 212013, Zhenjiang, China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 212013, Zhenjiang, China
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187
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Gumanova NG, Vasilyev DK, Bogdanova NL, Havrichenko YI, Kots AY, Metelskaya VA. Application of an antibody microarray for serum protein profiling of coronary artery stenosis. Biochem Biophys Res Commun 2022; 631:55-63. [PMID: 36166954 DOI: 10.1016/j.bbrc.2022.09.053] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
Protein expression profiling in the serum is used to identify novel biomarkers and investigate the signaling pathways in various diseases. The aim of the present study was to evaluate serum biomarkers associated with coronary artery stenosis resulting from atherosclerosis. The study included 4 groups of subjects: group A and B with and without coronary lesions, respectively, were selected from a previously reported cohort study on coronary atherosclerosis, control group C comprised of asymptomatic subjects and group D was used for independent validation of the microarray data by ELISA. Labeled serum proteins were profiled by an Explorer antibody array, which included 656 specific antibodies in two replicates (FullMoon Biosystems, USA). Cadherin-P, interleukin-5, glutathione S-transferase Mu, and neuronal nitric oxide synthase were sex-independently increased in Group A compared with those in group B. The microarray data on cadherin-P were externally validated in an independent group D using ELISA. Fibroblast growth factor-1, FGF-2, collagen II, granulocyte-macrophage colony-stimulating factor, IL-1 alpha, angiopoietin-2, granulocyte colony-stimulating factor, lymphocyte cell-specific protein tyrosine kinase, and IkappaB kinase b were increase in men in group A compared with group B. Cyclin-dependent kinase 1, DNA fragmentation factor subunit alpha DFF45/ICAD, adenovirus type 2 E1A, calponin, ADP-ribosylation factor-6, muscle-specific actin, thyroid hormone receptor alpha, and alpha-methylacyl-CoA racemase were specifically increased in women in Group A compared with group B. Alterations in the levels of specific proteins may point to the signaling pathways contributing to coronary atherosclerosis, and these proteins will be useful biomarkers for the progression of cardiovascular diseases.
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Affiliation(s)
- Nadezhda G Gumanova
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation.
| | - Dmitry K Vasilyev
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Natalya L Bogdanova
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Yaroslav I Havrichenko
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Alexander Ya Kots
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Victoria A Metelskaya
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
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188
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Cai L, Yang F, Wang Y, Yang J, Zhu Y, Ma X, Höfer J, Wang Y, Ma Y, Xiao L. A combined protein toxin screening based on the transcriptome and proteome of Solenopsis invicta. Proteome Sci 2022; 20:15. [PMID: 36131344 PMCID: PMC9494847 DOI: 10.1186/s12953-022-00197-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background Multi-omics technology provides a good tool to analyze the protein toxin composition and search for the potential pathogenic factors of Solenopsis invicta, under the great harm of the accelerated invasion in southern China. Methods Species collection, functional annotation, toxin screening, and 3D modeling construction of three interested toxins were performed based on the successfully constructed transcriptome and proteome of S. invicta. Results A total of 33,231 unigenes and 721 proteins were obtained from the constructed transcriptome and proteome, of which 9,842 (29.62%) and 4,844 (14.58%) unigenes, as well as 469 (65.05%) and 71 (99.45%) proteins were annotated against the databases of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, respectively. After comparing with the uniprot toxin database, a total of 316 unigenes and 47 proteins (calglandulin, venom allergen 3, and venom prothrombin activator hopsarin-D, etc.) were successfully screened. Conclusions The update of annotations at the transcriptome and proteome levels presents a progression in the comprehension of S. invicta in China. We also provide a protein toxin list that could be used for further exploration of toxicity as well as its antagonistic strategy by S. invicta. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-022-00197-z.
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Affiliation(s)
- Liuyang Cai
- Basic School of Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China
| | - Fengling Yang
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, 130118, Jilin, China.,Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China
| | - Yongfang Wang
- Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China
| | - Jishun Yang
- Medical Insurance Center, Navy Medical Center, Navy Medical Center of PLA, Shanghai, 200050, China
| | - Yina Zhu
- Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China
| | - Xueqi Ma
- Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China
| | - Juan Höfer
- Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, 2340000, Región de Valparaíso, Chile
| | - Yichao Wang
- Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China. .,Department of Clinical Laboratory, Taizhou Central Hospital, Taizhou, 318000, Zhejiang, China.
| | - Yajun Ma
- Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China.
| | - Liang Xiao
- Faculty of Naval Medicine, Second Military Medical University (Naval Medical University), Shanghai, 200433, China.
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189
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Andronis CE, Jacques S, Lipscombe R, Tan KC. Comparative sub-cellular proteome analyses reveals metabolic differentiation and production of effector-like molecules in the dieback phytopathogen Phytophthora cinnamomi. J Proteomics 2022; 269:104725. [PMID: 36096432 DOI: 10.1016/j.jprot.2022.104725] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/23/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022]
Abstract
Phytopathogenic oomycetes pose a significant threat to global biodiversity and food security. The proteomes of these oomycetes likely contain important factors that contribute to their pathogenic success, making their discovery crucial for elucidating pathogenicity. Phytophthora cinnamomi is a root pathogen that causes dieback in a wide variety of crops and native vegetation world-wide. Virulence proteins produced by P. cinnamomi are not well defined and a large-scale approach to understand the biochemistry of this pathogen has not been documented. Soluble mycelial, zoospore and secreted proteomes were obtained and label-free quantitative proteomics was used to compare the composition of the three sub-proteomes. A total of 4635 proteins were identified, validating 17.7% of the predicted gene set. The mycelia were abundant in transporters for nutrient acquisition, metabolism and cellular proliferation. The zoospores had less metabolic related ontologies but were abundant in energy generating, motility and signalling associated proteins. Virulence-associated proteins were identified in the secretome such as candidate effector and effector-like proteins, which interfere with the host immune system. These include hydrolases, cell wall degrading enzymes, putative necrosis-inducing proteins and elicitins. The secretome elicited a hypersensitive response on the roots of a model host and thus suggests evidence of effector activity. SIGNIFICANCE: Phytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and several horticultural crops such as avocado, pineapple and macadamia. Whilst this pathogen has significance world-wide, its pathogenicity and virulence have not been described in depth. We carried out comparative label-free proteomics of the mycelia, zoospores and secretome of P. cinnamomi. This study highlights the differential metabolism and cellular processes between the sub-proteomes. Proteins associated with metabolism, nutrient transport and cellular proliferation were over represented in the mycelia. The zoospores have a specialised proteome showing increased energy generation geared towards motility. Candidate effectors and effector-like secreted proteins were also identified, which can be exploited for genetic resistance. This demonstrates a better understanding of the biology and pathogenicity of P. cinnamomi infection that can subsequently be used to develop effective methods of disease management.
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Affiliation(s)
- Christina E Andronis
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia; Proteomics International, Nedlands, WA, Australia.
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia
| | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia.
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190
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Guatelli S, Ferrario C, Bonasoro F, Anjo SI, Manadas B, Candia Carnevali MD, Varela Coelho A, Sugni M. More than a simple epithelial layer: multifunctional role of echinoderm coelomic epithelium. Cell Tissue Res 2022. [PMID: 36083358 DOI: 10.1007/s00441-022-03678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 08/23/2022] [Indexed: 11/02/2022]
Abstract
In echinoderms, the coelomic epithelium (CE) is reportedly the source of new circulating cells (coelomocytes) as well as the provider of molecular factors such as immunity-related molecules. However, its overall functions have been scarcely studied in detail. In this work, we used an integrated approach based on both microscopy (light and electron) and proteomic analyses to investigate the arm CE in the starfish Marthasterias glacialis during different physiological conditions (i.e., non-regenerating and/or regenerating). Our results show that CE cells share both ultrastructural and proteomic features with circulating coelomocytes (echinoderm immune cells). Additionally, microscopy and proteomic analyses indicate that CE cells are actively involved in protein synthesis and processing, and membrane trafficking processes such as phagocytosis (particularly of myocytes) and massive secretion phenomena. The latter might provide molecules (e.g., immune factors) and fluids for proper arm growth/regrowth. No stem cell marker was identified and no pre-existing stem cell was observed within the CE. Rather, during regeneration, CE cells undergo dedifferentiation and epithelial-mesenchymal transition to deliver progenitor cells for tissue replacement. Overall, our work underlines that echinoderm CE is not a "simple epithelial lining" and that instead it plays multiple functions which span from immunity-related roles as well as being a source of regeneration-competent cells for arm growth/regrowth.
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191
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van Son M, Våge DI, Skaugen M, Tremoen NH, Gaustad AH, Zeremichael TT, Myromslien FD, Grindflek E. Protein profiling of testicular tissue from boars with different levels of hyperactive sperm motility. Acta Vet Scand 2022; 64:21. [PMID: 36064611 PMCID: PMC9446748 DOI: 10.1186/s13028-022-00642-1] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022] Open
Abstract
Hyperactive sperm motility is important for successful fertilization. In the present study, a proteome profiling approach was performed to identify the differences between Landrace boars with different levels of hyperactive sperm motility in liquid extended semen. Two contrasts were studied: (i) high versus low levels of sperm hyperactivity at semen collection day and (ii) high versus low change in levels of sperm hyperactivity after 96 h semen storage. Testicular samples were analyzed on a Q Exactive mass spectrometer and more than 6000 proteins were identified in the 13 samples. The most significant differentially expressed proteins were mediator complex subunit 28 (MED28), cell division cycle 37 like 1 (CDC37L1), ubiquitin specific peptidase 10 (USP10), zinc finger FYVE-type containing 26 (ZFYVE26), protein kinase C delta (PRKCD), actinin alpha 4 (ACTN4), N(alpha)-acetyltransferase 30 (NAA30), C1q domain-containing (LOC110258309) and uncharacterized LOC100512926. Of the differentially expressed proteins, 11 have previously been identified as differentially expressed at the corresponding mRNA transcript level using the same samples and contrasts. These include sphingosine kinase 1 isoform 2 (SPHK1), serine and arginine rich splicing factor 1 (SRSF1), and tubulin gamma-1 (TUBG1) which are involved in the acrosome reaction and sperm motility. A mass spectrometry approach was applied to investigate the protein profiles of boars with different levels of hyperactive sperm motility. This study identified several proteins previously shown to be involved in sperm motility and quality, but also proteins with no known function for sperm motility. Candidates that are differentially expressed on both mRNA and protein levels are especially relevant as biological markers of semen quality.
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Affiliation(s)
| | - Dag Inge Våge
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Morten Skaugen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Nina Hårdnes Tremoen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, Ås, Norway.,Department of Biotechnology, Inland Norway University of Applied Sciences, 2318, Hamar, Norway
| | - Ann Helen Gaustad
- Norsvin, Storhamargata 44, 2317, Hamar, Norway.,Department of Biotechnology, Inland Norway University of Applied Sciences, 2318, Hamar, Norway
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192
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Blasco Tavares Pereira Lopes F, Schlatzer D, Wang R, Li X, Feng E, Koyutürk M, Qi X, Chance MR. Temporal and Sex-Linked Protein Expression Dynamics in a Familial Model of Alzheimer's Disease. Mol Cell Proteomics 2022; 21:100280. [PMID: 35944844 PMCID: PMC9483563 DOI: 10.1016/j.mcpro.2022.100280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Mouse models of Alzheimer's disease (AD) show progression through stages reflective of human pathology. Proteomics identification of temporal and sex-linked factors driving AD-related pathways can be used to dissect initiating and propagating events of AD stages to develop biomarkers or design interventions. In the present study, we conducted label-free proteome measurements of mouse hippocampus tissue with variables of time (3, 6, and 9 months), genetic background (5XFAD versus WT), and sex (equal males and females). These time points are associated with well-defined phenotypes with respect to the following: Aβ42 plaque deposition, memory deficits, and neuronal loss, allowing correlation of proteome-based molecular signatures with the mouse model stages. Our data show 5XFAD mice exhibit increases in known human AD biomarkers as amyloid-beta peptide, APOE, GFAP, and ITM2B are upregulated across all time points/stages. At the same time, 23 proteins are here newly associated with Alzheimer's pathology as they are also dysregulated in 5XFAD mice. At a pathways level, the 5XFAD-specific upregulated proteins are significantly enriched for DNA damage and stress-induced senescence at 3-month only, while at 6-month, the AD-specific proteome signature is altered and significantly enriched for membrane trafficking and vesicle-mediated transport protein annotations. By 9-month, AD-specific dysregulation is also characterized by significant neuroinflammation with innate immune system, platelet activation, and hyper-reactive astrocyte-related enrichments. Aside from these temporal changes, analysis of sex-linked differences in proteome signatures uncovered novel sex and AD-associated proteins. Pathway analysis revealed sex-linked differences in the 5XFAD model to be involved in the regulation of well-known human AD-related processes of amyloid fibril formation, wound healing, lysosome biogenesis, and DNA damage. Verification of the discovery results by Western blot and parallel reaction monitoring confirm the fundamental conclusions of the study and poise the 5XFAD model for further use as a molecular tool for understanding AD.
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Affiliation(s)
- Filipa Blasco Tavares Pereira Lopes
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Daniela Schlatzer
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rihua Wang
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiaolin Li
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Emily Feng
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mehmet Koyutürk
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xin Qi
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark R Chance
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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193
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Rodriguez-Martinez H, Roca J. Extracellular vesicles in seminal plasma: A safe and relevant tool to improve fertility in livestock? Anim Reprod Sci 2022; 244:107051. [PMID: 35933831 DOI: 10.1016/j.anireprosci.2022.107051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/01/2022]
Abstract
Seminal plasma (SP) is not a pre-requisite for pregnancy. Yet, this heterogeneous, composite SP has proven relevant for fertility, as mediator for cell-to-cell communication between producing cells, spermatozoa and the female internal genital tract, regulating complex reproductive processes. Bearing hormones, proteins, cytokines as well as nuclei acids in nano-sized lipid bilayer seminal extracellular vesicles (sEVs), the SP concerts signaling to the female. Signals influence timing of ovulation, sperm transport and, particularly, enable the female immune system to balance her cryptic choice to engage into pregnancy or reject an eventual fertilization. This essay, focusing on livestock in general and pigs in particular, discusses the intrinsic roles of sEVs with regards to reproductive homeostasis, while binding and internalizing their cargo in spermatozoa and female tract epithelia to regulate their functional activity. Since prior studies had inconclusive results using bulk SP or single SP-contained free molecules, argumentation is hereby provided to increase the current incipient research on livestock sEVs, where fragile molecules relevant for fertility are shielded from degradation during handling. Seminal EVs isolated from SP can be used for andrological diagnosis and perhaps to select breeders with optimal fertility. Moreover, sEVs can be laboratory-uploaded with specific molecules or even engineered as lipid nanodroplets used as additives for extenders to improve fertility after artificial insemination (AI) or reproductive biotechnologies.
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Affiliation(s)
- Heriberto Rodriguez-Martinez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden.
| | - Jordi Roca
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", University of Murcia, Murcia, Spain
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194
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Ding C, Song L, Li Y, Shen L, Liu D, Wang F, Lin Z, Yang J. Proteome-wide analysis of lysine 2-hydroxyisobutyrylation in Frankliniella occidentalis. BMC Genomics 2022; 23:621. [PMID: 36038823 PMCID: PMC9422105 DOI: 10.1186/s12864-022-08841-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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysine 2-hydroxyisobutyrylation (Khib) is a novel and conserved post-translational modification (PTM). Frankliniella occidentalis are economically important agricultural pests globally and also notorious for vectoring destructive plant viruses. To better study the disease transmission mechanism of F. occidentalis, it is necessary to conduct in-depth analysis of it. So far, no Khib modification of insects has been reported. RESULTS In this study, a proteome-wide analysis of Khib modifications in F. occidentalis was analyzed for the first time through the combination of high performance liquid chromatography fractionation technology and 2-hydroxyisobutyrylated peptide enrichment and other advanced technologies, 4093 Khib sites were identified on 1125 modified proteins. Bioinformatics and functional enrichment analyses showed that Khib-modified proteins were significantly enriched in many cell compartments and pathways, especially related to various cellular components and biological processes, and were more concentrated in ribosomes and proteasome subunits, involved in energy metabolism, protein synthesis and degradation, compared to the other nine species including Japonica rice, Homo sapiens, P. patens, Botrytis, Ustilaginoidea virens, Saccharomyces cerevisiae, T. gondii, C. albicans, and F. oxysporum. And Khib sites on virus-interacting insect proteins were discovered for the first time, such as cyclophilin and endoCP-GN. CONCLUSIONS After three repeated experiments, we found a total of 4093 Khib sites on 1125 proteins. These modified proteins are mainly concentrated in ribosomes and proteasome subunits, and are widely involved in a variety of critical biological activities and metabolic processes of F. occidentalis. In addition, for the first time, Khib modification sites are found on the proteome of F. occidentalis, and these sites could be acted as for the virus interaction, including cyclophilin and endoCP-GN. The global map of 2-hydroxyisobutyrylation in thrips is an invaluable resource to better understand the biological processes of thrips and provide new means for disease control and mitigation of pest damage to crops.
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Affiliation(s)
- Chengying Ding
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Liyun Song
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Dongyang Liu
- Liangshan State Company of Sichuan Province Tobacco Company, Liangshan, 615000, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhonglong Lin
- Country Yunnan Province Company of China Tobacco Corporation, Kunming, 650001, China.
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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195
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Yakovleva G, Kurdy W, Gorbunova A, Khilyas I, Lochnit G, Ilinskaya O. Bacillus pumilus proteome changes in response to 2,4,6-trinitrotoluene-induced stress. Biodegradation 2022; 33:593-607. [PMID: 35980495 DOI: 10.1007/s10532-022-09997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022]
Abstract
2,4,6-Trinitrotoluene (TNT) is the most widely used nitroaromatic compound and is highly resistant to degradation. Most aerobic microorganisms reduce TNT to amino derivatives via formation of nitroso- and hydroxylamine intermediates. Although pathways of TNT degradation are well studied, proteomic analysis of TNT-degrading bacteria was done only for some individual Gram-negative strains. Here, we isolated a Gram-positive strain from TNT-contaminated soil, identified it as Bacillus pumilus using 16S rRNA sequencing, analyzed its growth, the level of TNT transformation, ROS production, and revealed for the first time the bacillary proteome changes at toxic concentration of TNT. The transformation of TNT at all studied concentrations (20-200 mg/L) followed the path of nitro groups reduction with the formation of 4-amino-2,6-dinitrotoluene. Hydrogen peroxide production was detected during TNT transformation. Comparative proteomic analysis of B. pumilus showed that TNT (200 mg/L) inhibited expression of 46 and induced expression of 24 proteins. Among TNT upregulated proteins are those which are responsible for the reductive pathway of xenobiotic transformation, removal of oxidative stress, DNA repair, degradation of RNA and cellular proteins. The production of ribosomal proteins, some important metabolic proteins and proteins involved in cell division are downregulated by this xenobiotic.
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Affiliation(s)
- Galina Yakovleva
- Microbiology Department, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlevskaya St., 18, Tatarstan, Kazan, Russia, 420008
| | - William Kurdy
- Microbiology Department, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlevskaya St., 18, Tatarstan, Kazan, Russia, 420008
| | - Anna Gorbunova
- Microbiology Department, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlevskaya St., 18, Tatarstan, Kazan, Russia, 420008
| | - Irina Khilyas
- Microbiology Department, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlevskaya St., 18, Tatarstan, Kazan, Russia, 420008
| | - Guenter Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Friedrichstrasse 24, Giessen, Germany, 35392
| | - Olga Ilinskaya
- Microbiology Department, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlevskaya St., 18, Tatarstan, Kazan, Russia, 420008.
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196
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Egorova DA, Solovyev AI, Polyakov NB, Danilova KV, Scherbakova AA, Kravtsov IN, Dmitrieva MA, Rykova VS, Tutykhina IL, Romanova YM, Gintsburg AL. Biofilm matrix proteome of clinical strain of P. aeruginosa isolated from bronchoalveolar lavage of patient in intensive care unit. Microb Pathog 2022; 170:105714. [PMID: 35973647 DOI: 10.1016/j.micpath.2022.105714] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/30/2022] [Accepted: 08/04/2022] [Indexed: 10/15/2022]
Abstract
Extracellular matrix plays a pivotal role in biofilm biology and proposed as a potential target for therapeutics development. As matrix is responsible for some extracellular functions and influence bacterial cytotoxicity against eukaryotic cells, it must have unique protein composition. P. aeruginosa is one of the most important pathogens with emerging antibiotic resistance, but only a few studies were devoted to matrix proteomes and there are no studies describing matrix proteome for any clinical isolates except reference strains PAO1 and ATCC27853. Here we report the first biofilm matrix proteome of P. aeruginosa isolated from bronchoalveolar lavage of patient in intensive care unit. We have identified the largest number of proteins in the matrix among all published studies devoted to P. aeruginosa biofilms. Comparison of matrix proteome with proteome from embedded cells let us to identify several enriched bioprocess groups. Bioprocess groups with the largest number of overrepresented in matrix proteins were oxidation-reduction processes, proteolysis, and transmembrane transport. The top three represented in matrix bioprocesses concerning the size of the GO annotated database were cell redox homeostasis, nucleoside metabolism, and fatty acid synthesis. Finally, we discuss the obtained data in a prism of antibiofilm therapeutics development.
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Affiliation(s)
- Daria A Egorova
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1).
| | - Andrey I Solovyev
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Nikita B Polyakov
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Ksenya V Danilova
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Anastasya A Scherbakova
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Ivan N Kravtsov
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Maria A Dmitrieva
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Valentina S Rykova
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Irina L Tutykhina
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1)
| | - Yulia M Romanova
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1); I.M. Sechenov First Moscow State Medical University, Moscow, 119992, Russia(2)
| | - Alexander L Gintsburg
- National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya, Russian Ministry of Health, Moscow, 123098, Russia(1); I.M. Sechenov First Moscow State Medical University, Moscow, 119992, Russia(2)
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197
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Lin H, Ma X, Yang X, Chen Q, Wen Z, Yang M, Fu J, Yin T, Lu G, Qi J, Han H, Yang Y. Natural shikonin and acetyl-shikonin improve intestinal microbial and protein composition to alleviate colitis-associated colorectal cancer. Int Immunopharmacol 2022; 111:109097. [PMID: 35952517 DOI: 10.1016/j.intimp.2022.109097] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/24/2022] [Accepted: 07/24/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) and inflammatory bowel disease (IBD) are the most common diseases of human digestive system. Nowadays, the influence of the inflammatory microenvironment on tumorigenesis has become a new direction, and the exploration of relative molecular mechanism will facilitate the discovery and identification of novel potential anti-cancer molecules. METHODS Natural shikonin (SK) and acetyl-shikonin (acetyl-SK) was administered to azoxymethane (AOM)/dextran sodium sulphate (DSS)-induced colitis-associated colorectal cancer (CAC) mice model by gavage to investigate their therapeutic effects. Moreover, fresh feces and colon tissues were collected for determining the function of SK and acetyl-SK on the gut microbes and protein expression, respectively. RESULTS Both SK and acetyl-SK decreased AOM/DSS-induced CAC, and regulated the intestinal flora structure in CAC mouse model. They, especially SK, improved species richness, evenness and diversity of intestinal flora, recovered the upregulated ratio of Firmicutes to Bacteroidota (F/B ratio) which symbolizes gut microbiota dysbiosis. SK and its derivative increased the beneficial bacteria g__norank_f__Muribaculaceae, Lactobacillus, Lachnospiraceae_NK4A136_Group, and reduced those harmful ones including Ileibacterium and Coriobacteriaceae UCG-002. Notably, AOM/DSS caused significant increase in the abundance of Ileibaterium valens and g__norank_f__norank_o__Clostridia_UCG-014, which were not previously reported in studies of colonic inflammation or cancer, and the disorder was reversed by 20 mg/kg of SK. In our current study, the action of SK and acetyl-SK is dose-dependent, and 20 mg/kg SK exhibited the most effective functions, even better than the positive drug mesalazine. Moreover, differential proteomics and ELISA results showed that SK could recover the increase of pro-inflammatory cytokines (including IL-1β, IL-6 and TNF-α), the upregulation of pyruvate kinase isozyme type M2 (PKM2) and some other proteins (mainly concentrated in transcriptional mis-regulation in cancer and IL-17 signaling pathways), and the downregulation of Aldh1b1-Acc3-Maoa and Μgt2b34-Aldh1a1-Aldh1a7 involved in Wnt/β-catenin signaling pathway. CONCLUSION Our study identified SK and acetyl-SK, especially SK, as potential preventive agents for CAC through regulating both gut microbes and pathways involved in inflammation and cancer such as Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Hongyan Lin
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Xiaopeng Ma
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiaorong Yang
- School of Biology and Geography Science, Yili Normal University, Yining 835000, China
| | - Qingqing Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jiangyan Fu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Guihua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hongwei Han
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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198
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Han T, Mi Z, Chen Z, Zhao J, Zhang H, Lv Y, Du S, Bu R, Zhou J, Li X, Sun Z, Chen Z, Song Y, Zhang J, Hao R, Ge S. Multi-omics analysis reveals the influence of tetracycline on the growth of ryegrass root. J Hazard Mater 2022; 435:129019. [PMID: 35523093 DOI: 10.1016/j.jhazmat.2022.129019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.
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Affiliation(s)
- Tao Han
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China; Postdoctoral Research Station, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhaorong Mi
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhe Chen
- College of Life Science, Qinghai Normal University, Xining 810008, China
| | - Jinjin Zhao
- The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Haiguang Zhang
- The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Yang Lv
- Shanghai Fengyuan Biotechnology Limited Company, Shanghai 200240, China
| | - Shouyang Du
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ruifang Bu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Junguo Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xinzheng Li
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhiqiang Sun
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhuo Chen
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yiting Song
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Jun Zhang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ruijuan Hao
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shidong Ge
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China.
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199
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Beliakova-Bethell N, Manousopoulou A, Deshmukh S, Mukim A, Richman DD, Garbis SD, Spina CA. Integrated proteomics and transcriptomics analyses identify novel cell surface markers of HIV latency. Virology 2022; 573:50-58. [PMID: 35714458 PMCID: PMC10427345 DOI: 10.1016/j.virol.2022.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
Elimination of the latent HIV cell reservoir may be possible, if the molecular identity of latently infected cells were fully elucidated. We conducted comprehensive molecular profiling, at the protein and RNA levels, of primary T cells latently infected with HIV in vitro. Isobaric labelling quantitative proteomics and RNA sequencing identified 1453 proteins and 618 genes, altered in latently infected cells compared to mock-infected controls (p < 0.05). Biomarker selection was based on results from integrated data analysis. Relative enrichment for latently infected cells was monitored using flow cytometric sorting and the HIV integrant assay. Antibodies against selected proteins, encoded by CEACAM1 and PLXNB2, enabled enrichment of latently infected cells from cell mixtures by 3-10 fold (5.8 average, p < 0.001), comparable to levels obtained with biomarkers reported previously. Individual biomarkers are likely linked to subsets of latently infected cells, and an extended antibody panel will be required to inclusively target the latent HIV reservoir.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA.
| | - Antigoni Manousopoulou
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Proteas Bioanalytics Inc., BioLabs at the Lundquist Institute, Torrance, CA, USA
| | | | - Amey Mukim
- University of California at San Diego, CA, USA
| | - Douglas D Richman
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA
| | - Spiros D Garbis
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK; Proteas Bioanalytics Inc., BioLabs at the Lundquist Institute, Torrance, CA, USA
| | - Celsa A Spina
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA; University of California at San Diego, CA, USA
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200
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Dietrich MA, Adamek M, Teitge F, Teich L, Jung-Schroers V, Malinowska A, Świderska B, Rakus K, Kodzik N, Chadzińska M, Karol H, Liszewska E, Ciereszko A. Proteomic analysis of carp seminal plasma provides insights into the immune response to bacterial infection of the male reproductive system. Fish Shellfish Immunol 2022; 127:822-835. [PMID: 35840052 DOI: 10.1016/j.fsi.2022.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Aeromonas salmonicida is recognized as a significant bacterial pathogen in ulcerative disease of cyprinid fish. However, the mechanism of immunity to these bacteria in common carp is still not well understood, especially the immune regulation in the gonad to bacterial infection. The aims of our study were to analyze changes in the seminal plasma proteome following A. salmonicida infection in carp males. The observed pathological changes in the tissue (liver, spleen, kidney and testis) morphology and upregulation of immune-related genes (tnfa2, il6a) confirmed the successful infection challenge. Using mass spectrometry-based label-free quantitative proteomics, we identified 1402 seminal plasma proteins, and 44 proteins (20 up- and 24 downregulated) were found to be differentially abundant between infected and control males. Most differentially abundant proteins were involved in the immune response mechanisms, such as acute phase response, complement activation and coagulation, inflammation, lipid metabolism, cell-cell and cell-matrix adhesion, creatine-phosphate biosynthesis and germ cell-Sertoli cell junction signaling. Bacterial infection also caused profound changes in expression of selected genes in the testis and hematopoietic organs, which contributed to changes in seminal proteins. The altered seminal proteins and bacterial proteins in seminal plasma may serve as valuable markers of infection in the testis.
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Affiliation(s)
- Mariola A Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland.
| | - Mikołaj Adamek
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany
| | - Felix Teitge
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany
| | - Lukas Teich
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany
| | - Verena Jung-Schroers
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Pawinskiego 5a, 02-106, Warszawa, Poland
| | - Bianka Świderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Pawinskiego 5a, 02-106, Warszawa, Poland
| | - Krzysztof Rakus
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Natalia Kodzik
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Magdalena Chadzińska
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Halina Karol
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Ewa Liszewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
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