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Stathopoulou KM, Georgakopoulos S, Tasoulis S, Plagianakos VP. Investigating the overlap of machine learning algorithms in the final results of RNA-seq analysis on gene expression estimation. Health Inf Sci Syst 2024; 12:14. [PMID: 38435719 PMCID: PMC10904690 DOI: 10.1007/s13755-023-00265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/05/2023] [Indexed: 03/05/2024] Open
Abstract
Advances in computer science in combination with the next-generation sequencing have introduced a new era in biology, enabling advanced state-of-the-art analysis of complex biological data. Bioinformatics is evolving as a union field between computer Science and biology, enabling the representation, storage, management, analysis and exploration of many types of data with a plethora of machine learning algorithms and computing tools. In this study, we used machine learning algorithms to detect differentially expressed genes between different types of cancer and showing the existence overlap to final results from RNA-sequencing analysis. The datasets were obtained from the National Center for Biotechnology Information resource. Specifically, dataset GSE68086 which corresponds to PMID:200,068,086. This dataset consists of 171 blood platelet samples collected from patients with six different tumors and healthy individuals. All steps for RNA-sequencing analysis (preprocessing, read alignment, transcriptome reconstruction, expression quantification and differential expression analysis) were followed. Machine Learning- based Random Forest and Gradient Boosting algorithms were applied to predict significant genes. The Rstudio statistical tool was used for the analysis.
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Affiliation(s)
- Kalliopi-Maria Stathopoulou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece
| | | | - Sotiris Tasoulis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece
| | - Vassilis P. Plagianakos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece
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2
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Dutilloy E, Arias AA, Richet N, Guise JF, Duban M, Leclere V, Selim S, Jacques P, Jacquard C, Clément C, Ait Barka E, Esmaeel Q. Bacillus velezensis BE2 controls wheat and barley diseases by direct antagonism and induced systemic resistance. Appl Microbiol Biotechnol 2024; 108:64. [PMID: 38189957 DOI: 10.1007/s00253-023-12864-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/19/2023] [Accepted: 11/05/2023] [Indexed: 01/09/2024]
Abstract
Wheat and barley rank among the main crops cultivated on a global scale, providing the essential nutritional foundation for both humans and animals. Nevertheless, these crops are vulnerable to several fungal diseases, such as Septoria tritici blotch and net blotch, which significantly reduce yields by adversely affecting leaves and grain quality. To mitigate the effect of these diseases, chemical fungicides have proven to be genuinely effective; however, they impose a serious environmental burden. Currently, biocontrol agents have attracted attention as a sustainable alternative to fungicides, offering an eco-friendly option. The study aimed to assess the efficacy of Bacillus velezensis BE2 in reducing disease symptoms caused by Zymoseptoria tritici and Pyrenophora teres. This bacterium exhibited significant antagonistic effects in vitro by suppressing fungal development when pathogens and the beneficial strain were in direct confrontation. These findings were subsequently confirmed through microscopic analysis, which illustrated the strain's capacity to inhibit spore germination and mycelial growth in both pathogens. Additionally, the study analysed the cell-free supernatant of the bacterium using UPLC-MS (ultra-performance liquid chromatography-mass spectrometry). The results revealed that strain BE2 produces, among other metabolites, different families of cyclic lipopeptides that may be involved in biocontrol. Furthermore, the beneficial effects of strain BE2 in planta were assessed by quantifying the fungal DNA content directly at the leaf level after bacterization, using two different application methods (foliar and drenching). The results indicated that applying the beneficial bacterium at the root level significantly reduced pathogens pressure. Finally, gene expression analysis of different markers showed that BE2 application induced a priming effect within the first hours after infection. KEY POINTS: • BE2 managed Z. tritici and P. teres by direct antagonism and induced systemic resistance. • Strain BE2 produced seven metabolite families, including three cyclic lipopeptides. • Application of strain BE2 at the root level triggered plant defense mechanisms.
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Affiliation(s)
- Emma Dutilloy
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Anthony Arguëlles Arias
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Nicolas Richet
- Université de Reims Champagne Ardenne, Plateau Technique Mobile de Cytométrie Environnementale MOBICYTE, URCA/INERIS, UFR Sciences Exactes Et Naturelles, Reims, France
| | - Jean-François Guise
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Matthieu Duban
- Université de Lille, Université de Liège, UMRT, 1158 BioEcoAgro, Institut Charles Viollette, 59000, Lille, France
| | - Valérie Leclere
- Université de Lille, Université de Liège, UMRT, 1158 BioEcoAgro, Institut Charles Viollette, 59000, Lille, France
| | - Sameh Selim
- AGHYLE UP 2018.C101, SFR Condorcet FR CNRS 3417, Institut Polytechnique UniLaSalle, 19 Rue Pierre Waguet, BP 30313, F-60026, Beauvais Cedex, France
| | - Philippe Jacques
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Cédric Jacquard
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Christophe Clément
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Essaïd Ait Barka
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France.
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Cardoza RE, McCormick SP, Martínez-Reyes N, Rodríguez-Fernández J, Busman M, Proctor RH, Gutiérrez S. Analysis of substrate specificity of cytochrome P450 monooxygenases involved in trichothecene toxin biosynthesis. Appl Microbiol Biotechnol 2024; 108:1-21. [PMID: 38183477 PMCID: PMC10771604 DOI: 10.1007/s00253-023-12950-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 01/08/2024]
Abstract
Trichothecenes are a structurally diverse family of toxic secondary metabolites produced by certain species of multiple fungal genera. All trichothecene analogs share a core 12,13-epoxytrichothec-9-ene (EPT) structure but differ in presence, absence and types of substituents attached to various positions of EPT. Formation of some of the structural diversity begins early in the biosynthetic pathway such that some producing species have few trichothecene biosynthetic intermediates in common. Cytochrome P450 monooxygenases (P450s) play critical roles in formation of trichothecene structural diversity. Within some species, relaxed substrate specificities of P450s allow individual orthologs of the enzymes to modify multiple trichothecene biosynthetic intermediates. It is not clear, however, whether the relaxed specificity extends to biosynthetic intermediates that are not produced by the species in which the orthologs originate. To address this knowledge gap, we used a mutant complementation-heterologous expression analysis to assess whether orthologs of three trichothecene biosynthetic P450s (TRI11, TRI13 and TRI22) from Fusarium sporotrichioides, Trichoderma arundinaceum, and Paramyrothecium roridum can modify trichothecene biosynthetic intermediates that they do not encounter in the organism in which they originated. The results indicate that TRI13 and TRI22 could not modify the intermediates that they do not normally encounter, whereas TRI11 could modify an intermediate that it does not normally encounter. These findings indicate that substrate promiscuity varies among trichothecene biosynthetic P450s. One structural feature that likely impacts the ability of the P450s to use biosynthetic intermediates as substrates is the presence and absence of an oxygen atom attached to carbon atom 3 of EPT.
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Affiliation(s)
- Rosa E Cardoza
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, Ponferrada, 24400, Spain
| | - Susan P McCormick
- Agricultural Research Service, Mycotoxin Prevention and Applied Microbiology Research Unit, USDA, National Center for Agricultural Utilization Research, 1815 N University St, Peoria, IL, 61604, USA
| | - Natalia Martínez-Reyes
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, Ponferrada, 24400, Spain
| | | | - Mark Busman
- Agricultural Research Service, Mycotoxin Prevention and Applied Microbiology Research Unit, USDA, National Center for Agricultural Utilization Research, 1815 N University St, Peoria, IL, 61604, USA
| | - Robert H Proctor
- Agricultural Research Service, Mycotoxin Prevention and Applied Microbiology Research Unit, USDA, National Center for Agricultural Utilization Research, 1815 N University St, Peoria, IL, 61604, USA.
| | - Santiago Gutiérrez
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, Ponferrada, 24400, Spain.
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Sessa L, Oberti H, Abreo E, Pedrini N. Beauveria bassiana transcriptomics reveal virulence-associated shifts during insect lipid assimilation. Appl Microbiol Biotechnol 2024; 108:23. [PMID: 38159119 DOI: 10.1007/s00253-023-12898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 01/03/2024]
Abstract
Insect cuticular lipids, especially epicuticular hydrocarbons (CHC), have a significant role in insect ecology and interactions with other organisms, including fungi. The CHC composition of a specific insect species may influence the outcome of the interaction with a specific fungal strain. Some insects, such as Piezodorus guildinii, have low susceptibility towards fungal infections seemingly due to their CHC composition. The entomopathogenic fungus Beauveria bassiana can assimilate CHC and incorporate them as building blocks via cytochrome P450 monooxygenases (CYPs). However, little is known about other enzymes that promote the degradation/assimilation of these cuticular components. In this study, we performed a transcriptomic analysis to evaluate the in vitro response of two virulence-contrasting B. bassiana strains when grown on three different P. guildinii CHC sources. We found a different expression profile of virulence-related genes, as well as different GO and KEGG parameters enriched at 4 days post-inoculation, which could help account for the intrinsic virulence and for an alkane-priming virulence enhancement effect. The hypovirulent strain predominantly showed higher expression of cuticle penetration genes, including chitinases, proteases, and CYPs, with GO term categories of "heme binding," "monooxygenase activity," and "peroxisome" pathways enriched. The hypervirulent strain showed higher expression of cell wall remodeling and cell cycle genes, and cuticle adhesion and a distinct set of CYPs, with GO categories of "DNA-binding transcription factor activity" and KEGG pathways corresponding to "meiosis-yeast" and "cell cycle" enriched. These results suggest a delay and alternate routes in pathogenicity-related metabolism in the hypovirulent strain in comparison with the hypervirulent strain. KEY POINTS: •Transcriptomics of two B. bassiana strains grown in P. guildinii cuticular components •Virulence-related genes correlated with virulence enhancement towards P. guildinii •Differentially expressed genes, GOs and KEGGs showed different metabolic timelines associated with virulence.
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Affiliation(s)
- Lucia Sessa
- Laboratorio de Bioproducción, Plataforma de Bioinsumos. Instituto Nacional de Investigación Agropecuaria, estación experimental Wilson Ferreira Aldunate, Ruta 48, km, 10, Canelones, Uruguay
| | - Héctor Oberti
- Laboratorio de Bioproducción, Plataforma de Bioinsumos. Instituto Nacional de Investigación Agropecuaria, estación experimental Wilson Ferreira Aldunate, Ruta 48, km, 10, Canelones, Uruguay
| | - Eduardo Abreo
- Laboratorio de Bioproducción, Plataforma de Bioinsumos. Instituto Nacional de Investigación Agropecuaria, estación experimental Wilson Ferreira Aldunate, Ruta 48, km, 10, Canelones, Uruguay.
| | - Nicolas Pedrini
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CCT La Plata Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Nacional de La Plata (UNLP), calles 60 y 120, 1900, La Plata, Argentina.
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Ganhör C, Rezk M, Doppler C, Ruthmeier T, Wechselberger C, Müller M, Kotnik M, Puh Š, Messner B, Bernhard D. Aluminum, a colorful gamechanger: Uptake of an aluminum-containing food color in human cells and its implications for human health. Food Chem 2024; 442:138404. [PMID: 38237295 DOI: 10.1016/j.foodchem.2024.138404] [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: 08/09/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 02/15/2024]
Abstract
Aluminum is added to many food colors to change their solubility. This study compares the aluminum-containing food color carmine with its aluminum-free version carminic acid (both E 120), hypothesizing that the addition of aluminum does not only change the color's solubility, but also its effects on human cells. We could show that carmine, but not carminic acid, is taken up by gastrointestinal Caco-2 and umbilical vein endothelial cells (HUVEC). Clear differences between gene expression profiles of Caco-2 cells exposed to carmine, carminic acid or control were shown. KEGG analysis revealed that carmine-specific genes suppress oxidative phosphorylation, and showed that this suppression is associated with neurodegenerative diseases such as Alzheimer and Parkinson disease. Furthermore, carmine, but not carminic acid, increased proliferation of Caco-2 cells. Our findings show that a food color containing aluminum induces different cellular effects compared to its aluminum-free form, which is currently not considered in EU legislation.
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Affiliation(s)
- Clara Ganhör
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Marlene Rezk
- Experimental Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria.
| | - Christian Doppler
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Teresa Ruthmeier
- Cardiac Surgery Research Laboratory, Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria.
| | - Christian Wechselberger
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Marina Müller
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Michaela Kotnik
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Špela Puh
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Barbara Messner
- Cardiac Surgery Research Laboratory, Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria.
| | - David Bernhard
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria; Clinical Research Institute for Cardiovascular and Metabolic Diseases, Medical Faculty, Johannes Kepler University Linz, Linz, Austria.
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Oganezovi N, Lagani V, Kikvidze M, Gamkrelidze G, Tsverava L, Lepsveridze E, Kelly KM, Solomonia R. Long-term effects of myo-inositol on traumatic brain injury: Epigenomic and transcriptomic studies. IBRO Neurosci Rep 2024; 16:291-299. [PMID: 38374956 PMCID: PMC10875114 DOI: 10.1016/j.ibneur.2024.01.009] [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: 11/10/2023] [Accepted: 01/27/2024] [Indexed: 02/21/2024] Open
Abstract
Background and purpose Traumatic brain injury (TBI) and its consequences remain great challenges for neurology. Consequences of TBI are associated with various alterations in the brain but little is known about long-term changes of epigenetic DNA methylation patterns. Moreover, nothing is known about potential treatments that can alter these epigenetic changes in beneficial ways. Therefore, we have examined myo-inositol (MI), which has positive effects on several pathological conditions. Methods TBI was induced in mice by controlled cortical impact (CCI). One group of CCI animals received saline injections for two months (TBI+SAL), another CCI group received MI treatment (TBI+MI) for the same period and one group served as a sham-operated control. Mice were sacrificed 4 months after CCI and changes in DNA methylome and transcriptomes were examined. Results For the first time we: (i) provide comprehensive map of long-term DNA methylation changes after CCI in the hippocampus; (ii) identify differences by methylation sites between the groups; (iii) characterize transcriptome changes; (iv) provide association between DNA methylation sites and gene expression. MI treatment is linked with upregulation of genes covering 33 biological processes, involved in immune response and inflammation. In support of these findings, we have shown that expression of BATF2, a transcription factor involved in immune-regulatory networks, is upregulated in the hippocampus of the TBI+MI group where the BATF2 gene is demethylated. Conclusion TBI is followed by long-term epigenetic and transcriptomic changes in hippocampus. MI treatment has a significant effect on these processes by modulation of immune response and biological pathways of inflammation.
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Affiliation(s)
- Nino Oganezovi
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Vincenzo Lagani
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Marine Kikvidze
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Georgi Gamkrelidze
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Lia Tsverava
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
- Iv. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia
| | - Eka Lepsveridze
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Kevin M. Kelly
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States
- Department of Neurology, Philadelphia, PA, United States
- Department of Neurology, Allegheny General Hospital, Pittsburgh, PA, United States
- Center for Neuroscience Research, Allegheny Health Network Research Institute, Pittsburgh, PA, United States, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Revaz Solomonia
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
- Iv. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia
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Rohani Z, Sazegar H, Rahimi E. Unlocking the potential of Escherichia coli K-12: A novel approach for malignancy reduction in colorectal cancer through gene expression modulation. Gene 2024; 906:148266. [PMID: 38342251 DOI: 10.1016/j.gene.2024.148266] [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: 10/10/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
Studies have noted the association between Escherichia coli K-12 (E. coli K-12) and the reduction of malignancy in colorectal cancer (CRC). However, the molecular mechanisms underlying this relationship have not been thoroughly explored. The aim of this study was to identify the genes influenced by E. coli K-12 and their connection to CRC. We identified the genes affected by E. coli K-12 using the GSE50040 dataset. Additionally, we investigated the relationship between the expression of genes affected by E. coli K-12 and CRC using the cancer genome atlas data. The association between the expression of E. coli K-12-affected genes and patient prognosis was investigated using clinical data. Pathways related to CRC and E. coli K-12-related genes were analyzed using the Enrichr tool. Furthermore, we employed a protein-protein interaction (PPI) network to identify hub genes associated with both E. coli K-12 and CRC. To validate our findings, we conducted RT-qPCR analysis on CRC samples and adjacent normal tissue. The results of GSE50040 showed that E. coli K-12 could change the expression of many genes related to CRC in colorectal cell lines. The results showed that E. coli K-12 reduces the expression of several genes linked to the main pathways used by cancer cells, such as the metastasis, WNT, cell proliferation pathway, and mTORC1. It was demonstrated that elevated BGN, FJX1, and LZTS1 expression is linked to a bad prognosis in patients and that E. coli K-12 may be able to lower this expression. Also, based on the PPI network, genes such as KLF4 and CXCL3 were identified as hub genes related to genes affected by E. coli K-12. When KLF4 and CXCL3 expression levels in cancer samples were compared to nearby normal tissue, a significant change in these genes' expression levels was found in CRC. Our findings demonstrated the potential relationship between oncogene genes and genes impacted by E. coli K-12. Also, our findings demonstrated that E. coli K-12 may regulate the expression of genes linked to a high death rate. In summary, the results of this study suggest that E. coli K-12 can be regarded as a significant probiotic with the potential to mitigate the risk of CRC development.
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Affiliation(s)
- Zeinab Rohani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hossein Sazegar
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Ebrahim Rahimi
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Kadan-Jamal K, Jog A, Sophocleous M, Dotan T, Frumin P, Kuperberg Goshen T, Schuster S, Avni A, Shacham-Diamand Y. Sensing of gene expression in live cells using electrical impedance spectroscopy and DNA-functionalized gold nanoparticles. Biosens Bioelectron 2024; 252:116041. [PMID: 38401280 DOI: 10.1016/j.bios.2024.116041] [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: 10/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 02/26/2024]
Abstract
A novel electrical impedance spectroscopy-based method for non-destructive sensing of gene expression in living cells is presented. The approach used takes advantage of the robustness and responsiveness of electrical impedance spectroscopy and the highly specific and selective nature of DNA hybridization. The technique uses electrical impedance spectroscopy and gold nanoparticles functionalized with single-stranded DNA complementary to an mRNA of interest to provide reliable, real-time, and quantifiable data on gene expression in live cells. The system was validated by demonstrating specific detection of the uidA mRNA, which codes for the β-glucuronidase (GUS) enzyme, in Solanum lycopersicum MsK8 cells. Gold nanoparticles were functionalized with single-stranded DNA oligonucleotides consisting of either a sequence complementary to uidA mRNA or an arbitrary sequence. The DNA-functionalized gold nanoparticles were mixed with cell suspensions, allowing the gold nanoparticles to penetrate into the cells. The impedance spectra of suspensions of cells with gold nanoparticles inserted within them were then studied. In suspensions of uidA-expressing cells and gold nanoparticles functionalized with the complementary single-stranded DNA oligonucleotide, the impedance magnitude in the frequency range of interest was significantly higher (146 %) in comparison to all other controls. Due to its highly selective nature, the methodology has the potential to be used as a precision agricultural sensing system for accurate and real-time detection of markers of stress, viral infection, disease, and normal physiological activities.
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Affiliation(s)
- Kian Kadan-Jamal
- Department of Materials Science and Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Aakash Jog
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel.
| | - Marios Sophocleous
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Research & Development Department, eBOS Technologies Ltd., Nicosia, Cyprus
| | - Tali Dotan
- Department of Materials Science and Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Polina Frumin
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Silvia Schuster
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yosi Shacham-Diamand
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Scojen Institute of Synthetic Biology, Reichmann University, Herzliya, Israel
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Fakriadis I, Meiri-Ashkenazi I, Bracha C, Rosenfeld H, Corriero A, Zupa R, Pousis C, Papadaki M, Mylonas CC. Gonadotropin expression, pituitary and plasma levels in the reproductive cycle of wild and captive-reared greater amberjack (Seriola dumerili). Gen Comp Endocrinol 2024; 350:114465. [PMID: 38336122 DOI: 10.1016/j.ygcen.2024.114465] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
We compared the endocrine status of the pituitary-gonad axis of wild and captive-reared greater amberjack (Seriola dumerili) during the reproductive cycle (April - July), reporting on the expression and release of the two gonadotropins for the first time in the Mediterranean Sea. Ovaries from wild females were characterized histologically as DEVELOPING in early May and SPAWNING capable in late May-July, the latter having a 3 to 4-fold higher gonadosomatic index (GSI). SPAWNING capable wild females exhibited an increase in pituitary follicle stimulating hormone (Fsh) content, plasma testosterone (T) and 17,20β-dihydroxy-4-pregnen-3-one (17,20β-P), while almost a 10-fold increase was observed in pituitary luteinizing hormone (Lh) content. An increasing trend of plasma 17β-estradiol (E2) was also recorded between the two reproductive stages in wild females. Captive-reared females sampled during the reproductive cycle exhibited two additional reproductive categories, with REGRESSED females having extensive follicular atresia and fish in the REGENERATING stage having only primary oocytes in their ovaries. Pituitary content of Fsh and Lh, fshb and lhb expression and plasma levels of Fsh and Lh remained unchanged among the four reproductive stages in captive females, in contrast with plasma E2 and T that decreased in the REGENERATING stage, and 17,20β-P which increased after the DEVELOPING stage. In general, no significant hormonal differences were recorded between captive-reared and wild DEVELOPING females, in contrast to SPAWNING capable females, where pituitary Lh content, plasma Fsh and T were found to be lower in females in captivity. Overall, the captive females lagged behind in reproductive development compared to the wild ones and this was perhaps related to the multiple handling of the sea cages where all the sampled fish were maintained. Between wild males in the DEVELOPING and SPAWNING capable stages, pituitary Lh content, plasma T and 17,20β-P, and GSI exhibited 3 to 4-fold increases, while an increasing trend of pituitary Fsh content, lhb expression levels and plasma 11-ketotestosterone (11-KT) was also observed, and an opposite trend was observed in plasma Lh. Captive males were allocated to one more category, with REGRESSED individuals having no spermatogenic capacity. During the SPAWNING capable phase, almost all measured parameters were lower in captive males compared to wild ones. More importantly, captive males showed significant differences from their wild counterparts throughout the reproductive season, starting already from the DEVELOPING stage. Therefore, it appears that captivity already exerted negative effects in males prior to the onset of the study and the multiple handling of the cage where sampled fish were reared. Overall, the present study demonstrated that female greater amberjack do undergo full vitellogenesis in captivity, albeit with some dysfunctions that may be related to the husbandry of the experiment, while males, on the other hand, may be more seriously affected by captivity even before the onset of the study.
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Affiliation(s)
- Ioannis Fakriadis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, Heraklion, Crete 71003, Greece; University of Crete, Department of Biology, P.O. Box 2208, Heraklion 71409, Crete, Greece.
| | - Iris Meiri-Ashkenazi
- Israel Oceanographic and Limnological Research, National Center for Mariculture, Eilat 88112, Israel
| | - Chen Bracha
- Israel Oceanographic and Limnological Research, National Center for Mariculture, Eilat 88112, Israel
| | - Hanna Rosenfeld
- Israel Oceanographic and Limnological Research, National Center for Mariculture, Eilat 88112, Israel
| | - Aldo Corriero
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano (Bari), Italy
| | - Rosa Zupa
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano (Bari), Italy
| | | | - Maria Papadaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, Heraklion, Crete 71003, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, Heraklion, Crete 71003, Greece
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Huang X, Mao W, Yi Y, Lu Y, Liu F, Deng L. The effects of four paralogous piscidin antimicrobial peptides on the chemotaxis, macrophage respiratory burst, phagocytosis and expression of immune-related genes in orange-spotted grouper (Epinephelus coicodes). Dev Comp Immunol 2024; 154:105144. [PMID: 38316232 DOI: 10.1016/j.dci.2024.105144] [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: 08/30/2023] [Revised: 01/09/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Antimicrobial peptides (AMPs) are an essential part of the vertebrate innate immune system. Piscidins are a family of AMPs specific in fish. In our previous investigation, we identified four paralogous genes of piscidins in the orange-spotted grouper (Epinephelus coicodes), which exhibited distinct activities against bacteria, fungi, and parasitic ciliated protozoa. Piscidins demonstrated their capability to modulate the expression of diverse immune-related genes; however, their precise immunoregulatory functions remain largely unexplored. In this study, we examined the immunomodulatory properties of putative mature peptides derived from four E. coicodes piscidins (ecPis1S, ecPis2S, ecPis3S, and ecPis4S) in head kidney leukocytes (HKLs) or monocytes/macrophages (MO/MΦ)-like cells isolated from E. coicodes. Our data demonstrate that E. coicodes piscidins exhibit immunomodulatory activities supported by multiple lines of evidence. Firstly, all four piscidins displayed chemotactic activities towards HKLs, with the most potent chemotactic activity observed in ecPis2S. Secondly, stimulation with E. coicodes piscidins enhanced respiratory burst and phagocytic activity in MO/MФ-like cells, with ecPis3S showing the highest efficacy in increasing phagocytosis of MO/MΦ-like cells. Thirdly, mRNA expression levels of chemokine receptors, Toll-like receptors, T cell receptors, and proinflammatory cytokines were modulated to varying extents by the four piscidins in E. coicodes HKLs. Overall, our findings indicate that the immunological activities of these four paralogous piscidins from E. coicodes are exhibited in a paralog-specific and concentration-dependent manner, highlighting their distinct and versatile immunomodulatory properties. This study makes a significant contribution to the field of fish AMPs immunology by elucidating the novel mechanisms through which members of the piscidin family exert their immunomodulatory effects. Moreover, it provides valuable insights for further exploration of fish immunomodulating agents.
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Affiliation(s)
- Xiazi Huang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Wei Mao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Yonghao Yi
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Yubin Lu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Feihong Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Li Deng
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China.
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11
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Ateutchia-Ngouanet S, Nanfack-Minkeu F, Mavridis K, Wanji S, Demanou M, Vontas J, Djouaka R. Monitoring Aedes populations for arboviruses, Wolbachia, insecticide resistance and its mechanisms in various agroecosystems in Benin. Acta Trop 2024; 253:107178. [PMID: 38461924 DOI: 10.1016/j.actatropica.2024.107178] [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: 12/13/2023] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Aedes mosquitoes are the main vectors of arboviruses in Benin. Cases of dengue have been reported in Benin with all four serotypes of the virus actively circulating in this region. Some agricultural settings are known to harbor Aedes vectors responsible for the transmission of arboviruses. The massive use of certain insecticides in agricultural settings has probably contributed to insecticide resistance in these vectors. In Benin, the susceptibility of arbovirus vectors to insecticides is poorly studied. In addition, the distribution of Wolbachia spp., which is used against some arboviruses is unknown. Moreover, there is limited information regarding the vectors responsible for the transmission of arboviruses in Benin. This present study monitored the species composition, arboviruses, and Wolbachia symbiont status, as well as the phenotypic and molecular insecticide resistance profile of Aedes populations from three agroecosystems in Benin. Aedes species identification was performed morphologically and confirmed using qPCR. (RT)-qPCR assay was applied for monitoring the presence of DENV, CHIKV, ZIKV, and WNV pathogens as well as for naturally occurring Wolbachia symbionts. Insecticide resistance was assessed phenotypically, by permethrin (0.75%) exposure of Adults (F0) using World Health Organization (WHO) bioassay protocols, and at the molecular level, using TaqMan (RT)-qPCR assays for assessing knock-down resistance (kdr) mutations (F1534C, V1016G/I, and S989P) and the expression levels of eight detoxification genes (P450s from the CYP9 and CYP6 families, carboxylesterases and glutathione-S-transferases). Aedes aegypti (Ae. aegypti) mosquitoes were the most abundant (93.9%) in the three agroecosystems studied, followed by Aedes albopictus (Ae. albopictus) mosquitoes (6.1%). No arboviruses were detected in the study's mosquito populations. Naturally occurring Wolbachia symbionts were present in 7 pools out of 15 pools tested. This could influence the effectiveness of vector control strategies based on exogenously introduced Wolbachia, all present in the three agroecosystems. Full susceptibility to permethrin was observed in all tested populations of Ae. albopictus. On the contrary, Ae. aegypti were found to be resistant in all three agroecosystem sites except for banana plantation sites, where full susceptibility was observed. Molecular analysis revealed that individual target site resistance kdr mutations F1534C and V1016G/I were detected in most Ae. aegypti populations. Additionally, double mutant (F1534C + V1016G/I) mosquitoes were found in some populations, and in one case, triple mutant (F1534C + V1016G/I + S989P) mosquitoes were detected. Metabolic resistance, as reflected by overexpression of three P450 genes (CYP6BB2, CYP9J26, and CYP9J32), was also detected in Ae. aegypti mosquitoes. Our study provides information that could be used to strategize future vector control strategies and highlights the importance of continuing vector surveillance. Future studies should assess the effect of piperonyl butoxide (PBO) on metabolic resistance and identify the different strains of Wolbachia spp., to choose the best vector control strategies in Benin.
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Affiliation(s)
- S Ateutchia-Ngouanet
- International Institute of Tropical Agriculture (IITA), 08 Tri-Postal, P.O. Box 0932, Cotonou, Benin; Department Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. BOX 63, Buea, Cameroon.
| | - F Nanfack-Minkeu
- International Institute of Tropical Agriculture (IITA), 08 Tri-Postal, P.O. Box 0932, Cotonou, Benin; Department of Biology, The College of Wooster, OH, USA
| | - K Mavridis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - S Wanji
- Department Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. BOX 63, Buea, Cameroon
| | - M Demanou
- Regional Yellow Fever Laboratory Coordinator World Health Organization, Inter-Country Support Team West Africa, 03 PO BOX 7019 Ouagadougou 03, Burkina Faso
| | - J Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece; Department of Crop Science, Pesticide Science Laboratory, Agricultural University of Athens, Athens 11855, Greece
| | - R Djouaka
- International Institute of Tropical Agriculture (IITA), 08 Tri-Postal, P.O. Box 0932, Cotonou, Benin
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Sun M, Jing Y, Zhang T, Hu F, Chen Q, Liu G. Effect of salinity on the toxicokinetics, oxidative stress, and metallothionein gene expression in Meretrix meretrix exposed to cadmium. Comp Biochem Physiol C Toxicol Pharmacol 2024; 279:109863. [PMID: 38387688 DOI: 10.1016/j.cbpc.2024.109863] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/29/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
To understand the effect of salinity on the toxicokinetics, oxidative stress, and detoxification of cadmium-exposed Meretrix meretrix, M. meretrix were acclimatized to different salinities (8, 14, 20, 26, and 32 ppt) for 14 d, exposed to 10 μg/L Cd for 7 d, followed by a 28-day depuration period. The internal Cd concentration was determined, and the activities of antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and glutathione-S-transferase (GST)), and the malondialdehyde (MDA) content were measured. The mRNA expression levels of antioxidant enzyme (Cu/Zn SOD, CAT) and detoxification-related genes metallothionein (MT) were analyzed. The mean concentrations of Cd in M. meretrix tissues were in the order gill > digestive gland > mantle > axe foot. The Cd uptake rate in the four tissues decreased with increasing salinity (range: 14-26 ppt). The Cd elimination half-lives were the highest at 8 ppt and 14 ppt salinity. Cadmium activated the four oxidative stress-related related enzymes in the gills. At the end of accumulation period, Cd exposure at 20 ppt salinity significantly increased the expression of Cu/Zn SOD. CAT expression was significantly inhibited at 20 ppt salinity, but was induced at 32 ppt. MT mRNA expression was only induced under Cd at 20 ppt salinity. At the end of depuration period, Cu/Zn SOD expression was inhibited at salinities of 8, 14, and 26 ppt. The results indicated that SOD, CAT, GST, MDA, Cu/Zn SOD, CAT, and MT were sensitive to cadmium in a water environment, and can be used as indicators of marine heavy metal pollution.
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Affiliation(s)
- Ming Sun
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China.
| | - Yuanyuan Jing
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Tianwen Zhang
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Fanguang Hu
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Qun Chen
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Guangbin Liu
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China.
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13
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Marjan P, Martyniuk CJ, Arlos MJ, Servos MR, Ruecker NJ, Munkittrick KR. Identifying transcriptomic indicators of tertiary treated municipal effluent in longnose dace (Rhinichthys cataractae) caged under semi-controlled conditions in experimental raceways. Sci Total Environ 2024; 923:171257. [PMID: 38417510 DOI: 10.1016/j.scitotenv.2024.171257] [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: 09/15/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
To evaluate effects of tertiary treated wastewater treatment plant effluent (MWWE) on transcriptomic responses in longnose dace (Rhinichthys cataractae; LND) we conducted a semi-controlled study in experimental raceways (Advancing Canadian Water Assets facility) imbedded in the Pine Creek treatment plant (Calgary, AB). LND collected from a reference site in the Bow River (REF) were caged in raceways containing either 5 % Pine Creek effluent (PC) or Bow River water (BR; control) over 28 d. Liver transcriptomes were analyzed in males and females sampled on days 7, 14 and 28 from BR and PC, and compared to REF fish on day 0. Concurrent with the caging, selected environmental substances of concern were analyzed in the BR and PC. Significantly different unigenes (SDUs) in females (vs males) within both BR and PC raceways increased over time and compared to REF fish. Moreover, SDUs in females and males within the same treatment (i.e., BR, PC) showed a temporal increase as well as compared to REF fish. Time was the dominant factor affecting SDUs, whereas sex and treatment had less of an impact on the transcriptome profiling. Gene Set Enrichment Analysis of BR vs PC over time revealed effects on genes involved in growth, metabolism of carbohydrates and lipids, and immune system on day 7; however, by day 28, 80-100 % of the transcripts localized to enriched biomarkers were associated with tissue immune responses in both sexes. Exposure to 5 % effluent had significant effects on female liver somatic index but no effects were observed on other phenotypic health indices in either sex. BR was used as the source of reference water, but analyses showed trace amounts of ESOCs. Analyses did not point towards definitive response patterns that could be used in field-based ecotoxicogenomic studies on the impacts of well-treated MWWE but suggested compromised adaptive immune responses.
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Affiliation(s)
- Patricija Marjan
- University of Calgary, Department of Biological Sciences, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada.
| | - Christopher J Martyniuk
- University of Florida, Department of Physiological Sciences, College of Veterinary Medicine, 2187 Mowry Rd., Gainesville, FL 32611, USA
| | - Maricor J Arlos
- University of Alberta, Civil and Environmental Engineering, 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
| | - Mark R Servos
- University of Waterloo, Department of Biology, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Norma J Ruecker
- The City of Calgary, Water Services, UEP-Water Resources, 2100, Station M, #35B, Calgary, AB T2P 2M5, Canada
| | - Kelly R Munkittrick
- University of Calgary, Department of Biological Sciences, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
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Kumar RS, Datta T, Sinha H, Trivedi PK. Light-dependent expression and accumulation of miR408-encoded peptide, miPEP408, is regulated by HY5 in Arabidopsis. Biochem Biophys Res Commun 2024; 706:149764. [PMID: 38484569 DOI: 10.1016/j.bbrc.2024.149764] [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: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024]
Abstract
Recent studies propose that primary transcripts of miRNAs (pri-miRNAs) contain small Open Reading Frames (ORFs) capable of encoding miRNA-encoded peptides (miPEPs). These miPEPs can function as transcriptional regulators for their corresponding pri-miRNAs, ultimately enhancing mature miRNA accumulation. Notably, pri-miR408 encodes the functional peptide miPEP408, regulating expression of miR408 and its target genes, providing plant tolerance to stresses. While miPEPs are crucial regulators, the factors governing them are have not been studied in detail. Here, we explored the light-dependent regulation of miPEP408 in Arabidopsis. Expression analysis during dark-light transitions revealed light-induced transcription and accumulation of the miPEP408. As the promoter of miR408 contains cis-acting elements responsible for binding to the bZIP-type transcription factor ELONGATED HYPOCOTYL5 (HY5), known for light-mediated regulation in plants, we studied its involvement in the regulation of miR408. Analysis of HY5 mutant (hy5-215), complemented line (HY5OX/hy5), and CONSTITUTIVE PHOTOMORPHOGENIC 1 mutant (cop1-4) plants supported HY5's positive regulation of miPEP408. Grafting and GUS assays further suggested the role of HY5 as a shoot-root mobile signal inducing light-dependent miPEP408 expression. This study underscores the regulatory impact of light on small peptides, exemplified by miPEP408, mediated by the key transcription factor HY5.
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Affiliation(s)
- Ravi Shankar Kumar
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Tapasya Datta
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Hiteshwari Sinha
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prabodh Kumar Trivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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15
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Bashi MA, Ad'hiah AH. Molecular landscape of the interleukin-40 encoding gene, C17orf99, in patients with acute myeloid leukemia. Gene 2024; 904:148214. [PMID: 38286266 DOI: 10.1016/j.gene.2024.148214] [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: 11/17/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
Acute myeloid leukemia (AML) is a malignant hematological disorder in which aberrant cytokine signaling and inflammation play a role in disease initiation and progression. Interleukin-40 (IL-40) is a novel cytokine encoded by the chromosome 17 open reading frame 99 (C17orf99) gene. This cytokine is involved in mediating inflammation but its biological significance in the pathogenesis of AML has not been investigated. In this case-control and observational study, mRNA expression and DNA methylation of the C17orf99 gene were evaluated in the peripheral blood of AML patients. In addition, the polymorphism of two novel intergenic variants of the C17orf99 gene, rs2004339 A/G and rs2310998 G/A, were explored using a real-time polymerase chain reaction assay. The study was conducted on 131 patients with AML and 106 controls and gene expression and DNA methylation were expressed as fold-change (2-ΔΔCt). Results revealed that mRNA expression of the C17orf99 gene was down-regulated in AML patients, particularly in females, while up-regulated expression was found in patients with hypoalbuminemia. For DNA methylation, it was up-regulated in AML patients, particularly in females, AML M5 subtype, and CD4-negative and CD14-positive peripheral blood cells. The mutant A allele and the corresponding homozygous AA genotype of rs2004339 was significantly associated with an increased risk of AML. The AA genotype was also associated with significantly up-regulated C17orf99 mRNA expression and DNA methylation of compared to the wild-type GG genotype. In conclusions, C17orf99 mRNA expression showed down-regulated levels in the peripheral blood of AML patients, while DNA methylation was up-regulated. The intergenic variant rs2004339 was associated with susceptibility to AML and had an effect on mRNA expression and DNA methylation.
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Affiliation(s)
- Mustafa A Bashi
- Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Ali H Ad'hiah
- Tropical-Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.
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Montoya CA, Young W, Ryan L, Dunstan K, Peters J, Dewhurst H, Dekker J, Haggarty N, Dilger RN, Roy NC. The probiotic Lacticaseibacillus rhamnosus HN001 influences the architecture and gene expression of small intestine tissue in a piglet model. Br J Nutr 2024; 131:1289-1297. [PMID: 38053344 PMCID: PMC10950449 DOI: 10.1017/s0007114523002830] [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: 04/17/2023] [Revised: 10/25/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023]
Abstract
This study investigated the effects of Lacticaseibacillus rhamnosus HN001 supplementation on the architecture and gene expression in small intestinal tissues of piglets used as an animal model for infant humans. Twenty-four 10-d-old entire male piglets (4·3 (sd 0·59) kg body weight) were fed an infant formula (IF) (control) or IF supplemented with 1·3 × 105 (low dose) or 7·9 × 106 (high dose) colony-forming units HN001 per ml of reconstituted formula (n 8 piglets/treatment). After 24 d, piglets were euthanised. Samples were collected to analyse the histology and gene expression (RNAseq and qPCR) in the jejunal and ileal tissues, blood cytokine concentrations, and blood and faecal calprotectin concentrations. HN001 consumption altered (false discovery rate < 0·05) gene expression (RNAseq) in jejunal tissues but not in ileal tissues. The number of ileal goblet cells and crypt surface area increased quadratically (P < 0·05) as dietary HN001 levels increased, but no increase was observed in the jejunal tissues. Similarly, blood plasma concentrations of IL-10 and calprotectin increased linearly (P < 0·05) as dietary HN001 levels increased. In conclusion, supplementation of IF with HN001 affected the architecture and gene expression of small intestine tissue, blood cytokine concentration and frequencies, and blood calprotectin concentrations, indicating that HN001 modulated small intestinal tissue maturation and immunity in the piglet model.
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Affiliation(s)
- Carlos A. Montoya
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
- Riddet Institute, Massey University, Te Ohu Rangahau Kai Facility, Palmerston North4474, New Zealand
| | - Wayne Young
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
- Riddet Institute, Massey University, Te Ohu Rangahau Kai Facility, Palmerston North4474, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Fonterra Research and Development Centre, Dairy Farm Rd, Palmerston North, New Zealand
| | - Leigh Ryan
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - Kelly Dunstan
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - Jason Peters
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - Hilary Dewhurst
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - James Dekker
- Fonterra Research and Development Centre, Dairy Farm Rd, Palmerston North, New Zealand
| | - Neill Haggarty
- Fonterra Research and Development Centre, Dairy Farm Rd, Palmerston North, New Zealand
| | - Ryan N. Dilger
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Nicole C. Roy
- Riddet Institute, Massey University, Te Ohu Rangahau Kai Facility, Palmerston North4474, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
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Wang Z, Cui T, Wang Q. Optimization of degradation conditions and analysis of degradation mechanism for nitrite by Bacillus aryabhattai 47. Sci Total Environ 2024; 921:171096. [PMID: 38387569 DOI: 10.1016/j.scitotenv.2024.171096] [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: 12/06/2023] [Revised: 02/17/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Excessive nitrite levels cause significant damage to aquaculture, making it crucial to explore green and reliable nitrite removal technologies. In this study, A Bacillus aryabhattai (designated as the strain 47) isolated from aquaculture wastewater was used as the experimental strain. The nitrite degradation conditions of the strain 47 were optimized, and the optimal conditions are: glucose was 12.74 g/L, fermented special soybean meal was 21.27 g/L, MgCl2 369 mg/L, pH 7.0, incubated at 30 °C with the inoculum size of 2 % and the rotation speed of 170 rpm. Under the optimal conditions, the nitrite concentration of the culture solution was 200 mg/L, and the nitrite removal rate reached 91.4 %. Meanwhile, the mechanism by which Mg2+ enhanced the nitrite degradation ability of the strain 47 was investigated by transcriptomics. An operon structure directed cellular trafficking of Mg2+, and then, the Mg2+-mediated catalytic reaction of multiple enzymes enhanced and improved cellular metabolic processes (e.g. the transport and metabolism of nitrite, central carbohydrate metabolism oxidative phosphorylation). At the same time, with the progress of cell metabolism, cells secreted a series of enzymes related to nitrite transport and metabolism to promote the metabolism of nitrite. And the process of the assimilated nitrate reduction pathway of nitrite degradation in the strain 47 was elaborated at the transcriptome level. This study provided a new insight into nitrite treatment mediated by microbial organisms.
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Affiliation(s)
- Zhenhao Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Tangbing Cui
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Qiang Wang
- Guangdong Yuzanchen Biotechnology Co., Ltd, Jiangmen 529100, PR China
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18
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Navarro JM, Cárdenas L, Ortiz A, Figueroa Á, Morley SA, Vargas-Chacoff L, Leclerc JC, Détrée C. Testing the physiological capacity of the mussel Mytilus chilensis to establish into the Southern Ocean. Sci Total Environ 2024; 921:170941. [PMID: 38360303 DOI: 10.1016/j.scitotenv.2024.170941] [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: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
The Southern Ocean and the Antarctic Circumpolar Current create environmental conditions that serve as an efficient barrier to prevent the colonization of non-native species (NNS) in the marine ecosystems of Antarctica. However, warming of the Southern Ocean and the increasing number of transport opportunities are reducing the physiological and physical barriers, increasing the chances of NNS arriving. The aim of this study was to determine the limits of survival of the juvenile mussels, M. chilensis, under current Antarctic conditions and those projected under climate change. These assessments were used to define the mussels potential for establishment in the Antarctic region. Experimental mussels were exposed to four treatments: -1.5 °C (Antarctic winter), 2 °C (Antarctic summer), 4 °C (Antarctic projected) and 8 °C (control) for 80 days and a combination of physiological and transcriptomics approaches were used to investigate mussel response. The molecular responses of mussels were congruent with the physiological results, revealing tolerance to Antarctic winter temperatures. However, a higher number of regulated differentially expressed gene (DEGs) were reported in mussels exposed to Antarctic winter temperatures (-1.5 °C). This tolerance was associated with the activation of the biological processes associated with apoptosis (up regulated) and both cell division and cilium assembly (down regulated). The reduced feeding rate and the negative scope for growth, for a large part of the exposure period at -1.5 °C, suggests that Antarctic winter temperatures represents an environmental barrier to M. chilensis from the Magellanic region settling in the Antarctic. Although M. chilensis are not robust to current Antarctica thermal conditions, future warming scenarios are likely to weaken these physiological barriers. These results strongly suggest that the West Antarctic Peninsula could become part of Mytilus distributional range, especially with dispersal aided by increasing maritime transport activity across the Southern Ocean.
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Affiliation(s)
- Jorge M Navarro
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile.
| | - Leyla Cárdenas
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro Ortiz
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile
| | - Álvaro Figueroa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Simon A Morley
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile; Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral d Chile, Valdivia, Chile
| | - Jean-Charles Leclerc
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Camille Détrée
- Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA) Université de Caen-Normandie, CREC marine station, 54 rue du Docteur Charcot, 14530 Luc-sur-mer, France
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19
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Liu R, Hu B, Dannenmann M, Giesemann A, Geilfus CM, Li C, Gao L, Flemetakis E, Haensch R, Wang D, Rennenberg H. Significance of phosphorus deficiency for the mitigation of mercury toxicity in the Robinia pseudoacacia L.- rhizobia symbiotic association. J Hazard Mater 2024; 467:133717. [PMID: 38325100 DOI: 10.1016/j.jhazmat.2024.133717] [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: 10/29/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Nitrogen (N2)-fixing legumes can be used for phytoremediation of toxic heavy metal Mercury (Hg) contaminated soil, but N2-fixation highly relies on phosphorus (P) availability for nodule formation and functioning. Here, we characterized the significance of P deficiency for Hg accumulation and toxicity in woody legume plants. Consequences for foliar and root traits of rhizobia inoculation, Hg exposure (+Hg) and low P (-P) supply, individually and in combination were characterized at both the metabolite and transcriptome levels in seedlings of two Robinia pseudoacacia L. provenances originating from contrasting climate and soil backgrounds, i.e., GS in northwest and the DB in northeast China. Our results reveal that depleted P mitigates the toxicity of Hg at the transcriptional level. In leaves of Robinia depleted P reduced oxidative stress and improved the utilization strategy of C, N and P nutrition; in roots depleted P regulated the expression of genes scavenging oxidative stress and promoting cell membrane synthesis. Rhizobia inoculation significantly improved the performance of both Robinia provenances under individual and combined +Hg and -P by promoting photosynthesis, increasing foliar N and P content and reducing H2O2 and MDA accumulation despite enhanced Hg uptake. DB plants developed more nodules, had higher biomass and accumulated higher Hg amounts than GS plants and thus are suggested as the high potential Robinia provenance for future phytoremediation of Hg contaminated soils with P deficiency.
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Affiliation(s)
- Rui Liu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, China; College of Resources and Environment, Academy of Agriculture Sciences, Southwest University, Chongqing 400715, China
| | - Bin Hu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, China.
| | - Michael Dannenmann
- Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Karlsruhe Institute of Technology (KIT), Kreuzeckbahnstrasse 19, 82467 Garmisch-Partenkirchen, Germany
| | - Anette Giesemann
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany
| | - Christoph-Martin Geilfus
- Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, 65366 Geisenheim, Germany
| | - Canbo Li
- Shanghai OE Biotech. Co., Ltd., No. 1188, Lianhang Rd., Minhang district, Shanghai 201212, China
| | - Lan Gao
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, China; College of Resources and Environment, Academy of Agriculture Sciences, Southwest University, Chongqing 400715, China
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Robert Haensch
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, China; Institute for Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, D-38106 Braunschweig, Germany
| | - Dingyong Wang
- College of Resources and Environment, Academy of Agriculture Sciences, Southwest University, Chongqing 400715, China
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, China
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Weintraub Y, Cohen S, Yerushalmy-Feler A, Chapnik N, Tsameret S, Anafy A, Damari E, Ben-Tov A, Shamir R, Froy O. Circadian clock gene disruption in white blood cells of patients with celiac disease. Biochimie 2024; 219:51-54. [PMID: 37524198 DOI: 10.1016/j.biochi.2023.07.020] [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: 05/28/2023] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Clock gene disruption has been reported in inflammatory and autoimmune diseases. Specifically, it has been shown that clock gene expression is down-regulated in intestinal tissue and peripheral blood mononuclear cells of patients with inflammatory bowel disease (IBD). We aimed to determine the systemic expression of the circadian clock genes in newly diagnosed untreated, young patients with celiac disease (CeD). We prospectively enrolled patients younger than 20 years old who underwent diagnostic endoscopic procedures either for CeD diagnosis or due to other gastrointestinal complaints, at the pediatric and adult gastroenterology units, the Tel Aviv Sourasky Medical Center from 8/2016-8/2022. Demographic data, anthropometric parameters, and endoscopic macroscopic and microscopic findings were obtained. Blood samples were obtained to determine tissue transglutaminase (tTG) and core clock gene (CLOCK, BMAL1, PER1, PER2, CRY1, CRY2) expression in white blood cells (WBC). Thirty individuals were analyzed (18 with newly diagnosed CeD and 12 controls). Expression of the clock genes CLOCK, BMAL1, CRY2, PER1 and PER2 was significantly reduced in CeD patients compared to controls, while CRY1 did not differ between the groups. In conclusion, newly diagnosed, untreated, young patients with CeD have reduced clock gene expression in WBC compared to controls. These results suggest that, in CeD, the inflammatory response is associated with systemic disruption of clock gene expression, as is manifested in other inflammatory and autoimmune diseases. CLINICALTRIALS.GOV IDENTIFIER: NCT03662646.
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Affiliation(s)
- Y Weintraub
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - S Cohen
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Institute of Pediatric Gastroenterology, Dana-Dwek Children's Hospital, Sourasky Tel-Aviv Medical Center, Tel Aviv, Israel
| | - A Yerushalmy-Feler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Institute of Pediatric Gastroenterology, Dana-Dwek Children's Hospital, Sourasky Tel-Aviv Medical Center, Tel Aviv, Israel
| | - N Chapnik
- Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, Israel
| | - S Tsameret
- Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, Israel
| | - A Anafy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Institute of Pediatric Gastroenterology, Dana-Dwek Children's Hospital, Sourasky Tel-Aviv Medical Center, Tel Aviv, Israel
| | - E Damari
- Institute of Pediatric Gastroenterology, Dana-Dwek Children's Hospital, Sourasky Tel-Aviv Medical Center, Tel Aviv, Israel
| | - A Ben-Tov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Institute of Pediatric Gastroenterology, Dana-Dwek Children's Hospital, Sourasky Tel-Aviv Medical Center, Tel Aviv, Israel
| | - R Shamir
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - O Froy
- Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, Israel.
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21
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Qiu H, Chen Y, Fu J, Zhang C. Expression of ethylene biosynthetic genes during flower senescence and in response to ethephon and silver nitrate treatments in Osmanthus fragrans. Genes Genomics 2024; 46:399-408. [PMID: 38319456 DOI: 10.1007/s13258-023-01489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Sweet osmanthus (Osmanthus fragrans) is an ornamental evergreen tree species in China, whose flowers are sensitive to ethylene. The synthesis of ethylene is controlled by key enzymes and restriction enzymes, 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), which are encoded by multigene families. However, the key synthase responsible for ethylene regulation in O. fragrans is still unknown. OBJECTIVE This study aims to screen the key ethylene synthase genes of sweet osmanthus flowers in response to ethylene regulation. METHODS In this study, we used the ACO and ACS sequences of Arabidopsis thaliana to search for homologous genes in the O. fragrans petal transcriptome database. These genes were also analyzed bioinformatically. Finally, the expression levels of O. fragrans were compared before and after senescence, as well as after ethephon and silver nitrate treatments. RESULTS The results showed that there are five ACO genes and one ACS gene in O. fragrans transcriptome database, and the phylogenetic tree revealed that the proteins encoded by these genes had high homology to the ACS and ACO proteins in plants. Sequence alignment shows that the OfACO1-5 proteins have the 2OG-Fe(II) oxygenase domain, while OfACS1 contains seven conserved domains, as well as conserved amino acids in transaminases and glutamate residues related to substrate specificity. Expression analysis revealed that the expression levels of OfACS1 and OfACO1-5 were significantly higher at the early senescence stage compared to the full flowering stage. The transcripts of the OfACS1, OfACO2, and OfACO5 genes were upregulated by treatment with ethephon. However, out of these three genes, only OfACO2 was significantly downregulated by treatment with AgNO3. CONCLUSION Our study found that OfACO2 is an important synthase gene in response to ethylene regulation in sweet osmanthus, which would provide valuable data for further investigation into the mechanisms of ethylene-induced senescence in sweet osmanthus flowers.
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Affiliation(s)
- Hui Qiu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Yiwen Chen
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Jianxin Fu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
| | - Chao Zhang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
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22
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [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: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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23
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Georgoulis I, Papadopoulos DK, Lattos A, Michaelidis B, Feidantsis K, Giantsis IA. Increased seawater temperature triggers thermal, oxidative and metabolic response of Ostrea edulis, leading to anaerobiosis. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110943. [PMID: 38224830 DOI: 10.1016/j.cbpb.2024.110943] [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: 11/08/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
Bivalves are among the marine organisms most influenced by climate change. Despite the flat oyster's Ostrea edulis high economic value, its culture is developed on a very small scale, since this species possesses a strong susceptibility to abiotic stressors. Due to climate change, temperature is one of the most critical environmental parameters for the welfare of the Mediterranean basin's marine inhabitants. The present study's purpose was to investigate the physiological performance of the Mediterranean's native O. edulis as it faces exposure to different temperatures. Since juveniles are more susceptible to abiotic stressors, this experimental procedure was focused on young individuals. The seawater temperatures studied included a standard control temperature of 21 °C (often observed in several marine areas throughout the Mediterranean), as well as increased seawater temperatures of 25 °C and 28 °C, occasionally occurring in shallow Mediterranean waters inhabited by bivalve spat. These were selected since the tissues of O. edulis becomes partly anaerobic in temperatures exceeding 26 °C, while cardiac dysfunction (arrhythmia) emerges at 28 °C. The results demonstrate that temperatures above 25 °C trigger both the transcriptional upregulation of hsp70 and hsp90, and the antioxidant genes Cu/Zn sod and catalase. Enhancement of thermal tolerance and increased defense against increased ROS production during thermal stress, were observed. As the intensity and duration of thermal stress increases, apoptotic damage may also occur. The increased oxidative and thermal stress incurred at the highest temperature of 28 °C, seemed to trigger the switch from aerobic to anaerobic metabolism, reflected by higher pepck mRNA expressions and lower ETS activity.
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Affiliation(s)
- Ioannis Georgoulis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Dimitrios K Papadopoulos
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Athanasios Lattos
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | | | - Ioannis A Giantsis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, GR- 53100 Florina, Greece
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Barnard ME, Wang X, Petrick JL, Zirpoli GR, Jones D, Johnson WE, Palmer JR. Psychosocial stressors and breast cancer gene expression in the Black Women's Health Study. Breast Cancer Res Treat 2024; 204:327-340. [PMID: 38127176 DOI: 10.1007/s10549-023-07182-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Prior studies indicate that the physiologic response to stress can affect gene expression. We evaluated differential gene expression in breast cancers collected from Black women with high versus low exposure to psychosocial stressors. METHODS We analyzed tumor RNA sequencing data from 417 Black Women's Health Study breast cancer cases with data on early life trauma and neighborhood disadvantage. We conducted age-adjusted differential gene expression analyses and pathway analyses. We also evaluated Conserved Transcriptional Response to Adversity (CTRA) contrast scores, relative fractions of immune cell types, T cell exhaustion, and adrenergic signaling. Analyses were run separately for estrogen receptor positive (ER+; n = 299) and ER- (n = 118) cases. RESULTS Among ER+ cases, the top differentially expressed pathways by stress exposure were related to RNA and protein metabolism. Among ER- cases, they were related to developmental biology, signal transduction, metabolism, and the immune system. Targeted analyses indicated greater immune pathway enrichment with stress exposure for ER- cases, and possible relevance of adrenergic signaling for ER+ cases. CTRA contrast scores did not differ by stress exposure, but in analyses of the CTRA components, ER- breast cancer cases with high neighborhood disadvantage had higher pro-inflammatory gene expression (p = 0.039) and higher antibody gene expression (p = 0.006) compared to those with low neighborhood disadvantage. CONCLUSION There are multiple pathways through which psychosocial stress exposure may influence breast tumor biology. Given the present findings on inflammation and immune response in ER- tumors, further research to identify stress-induced changes in the etiology and progression of ER- breast cancer is warranted.
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Affiliation(s)
- Mollie E Barnard
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Xutao Wang
- Division of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Jessica L Petrick
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Dennis Jones
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA.
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25
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Sabalette KB, Campo VA, De Gaudenzi JG. Proteomic data of the Trypanosoma cruzi insect-dwelling epimastigotes overexpressing the RNA-binding protein UBP1. Data Brief 2024; 53:110085. [PMID: 38348324 PMCID: PMC10859248 DOI: 10.1016/j.dib.2024.110085] [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: 01/02/2024] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
We present data on the proteome of the Trypanosoma cruzi epimastigote cells overexpressing the U-rich RNA-binding protein 1 (UBP1). The role of this regulatory protein during the epimastigote-to-metacyclic trypomastigote stage transition was clearly established by our group at the transcriptome level; nevertheless, the impact of UBP1 overexpression on protein synthesis is not known. To address this question, we performed shotgun label-free quantification proteomics using an in vitro system based on the tetracycline-inducible expression of TcUBP1 and epimastigote wildtype cells. Using tryptic peptide digestion and LC-MS/MS analysis with Orbitrap technology, this data file describes the proteome of three biological samples per condition and yields 1637 correctly quantified proteins. The statistical comparisons of the two analyzed groups within the Proteome Discoverer platform identified 379 differentially expressed proteins, with 207 being up-regulated and 172 being down-regulated. In addition, profile plots and heatmap analysis to visualize the distribution of protein abundances within replicates are also presented. Data are available via ProteomeXchange with identifier PXD047761.
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Affiliation(s)
- Karina B. Sabalette
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A. Campo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
| | - Javier G. De Gaudenzi
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín - Consejo Nacional de Investigaciones Científicas y Técnicas, 1650 General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, 1650 General San Martín, Prov. de Buenos Aires, Argentina
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26
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Golozar M, Motlagh AV, Mahdevar M, Peymani M, InanlooRahatloo K, Ghaedi K. TBX15 and SDHB expression changes in colorectal cancer serve as potential prognostic biomarkers. Exp Mol Pathol 2024; 136:104890. [PMID: 38378070 DOI: 10.1016/j.yexmp.2024.104890] [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: 02/14/2023] [Revised: 01/07/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
Alterations in the expression of certain genes could be associated with both patient mortality rates and drug resistance. This study aimed to identify genes in colorectal cancer (CRC) that potentially serve as hub genes influencing patient survival rates. RNA-Seq data were downloaded from the cancer genome atlas database, and differential expression analysis was performed between tumors and healthy controls. Through the utilization of univariate and multivariate Cox regression analyses, in combination with the MCODE clustering module, the genes whose expression changes were related to survival rate and the hub genes related to them were identified. The mortality risk model was computed using the hub genes. CRC samples and the RT-qPCR method were utilized to confirm the outcomes. PharmacoGx data were employed to link the expression of potential genes to medication resistance and sensitivity. The results revealed the discovery of seven hub genes, which emerged as independent prognostic markers. These included HOXC6, HOXC13, HOXC8, and TBX15, which were associated with poor prognosis and overexpression, as well as SDHB, COX5A, and UQCRC1, linked to favorable prognosis and downregulation. Applying the risk model developed with the mentioned genes revealed a markedly higher incidence of deceased patients in the high-risk group compared to the low-risk group. RT-qPCR results indicated a decrease in SDHB expression and an elevation in TBX15 levels in cancer samples relative to adjacent healthy tissue. Also, PharmacoGx data indicated that the expression level of SDHB was correlated with drug sensitivity to Crizotinib and Dovitinib. Our findings highlight the potential association between alterations in the expression of genes such as HOXC6, HOXC13, HOXC8, TBX15, SDHB, COX5A, and UQCRC1 and increased mortality rates in CRC patients. As revealed by the PPI network, these genes exhibited the most connections with other genes linked to survival.
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Affiliation(s)
- Melika Golozar
- Kish International Campus, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Valipour Motlagh
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan 8165131378, Iran
| | - Mohammad Mahdevar
- Genius Gene, Genetics and Biotechnology Company, Tehran, Iran; Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kolsoum InanlooRahatloo
- Kish International Campus, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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Hussein S, Soliman NA, Dahmy SIE, Khamis T, Sameh R, Mostafa FM. Effectiveness of cannabidiol (CBD) on histopathological changes and gene expression in hepatocellular carcinoma (HCC) model in male rats: the role of Hedgehog (Hh) signaling pathway. Histochem Cell Biol 2024; 161:337-343. [PMID: 38296878 DOI: 10.1007/s00418-023-02262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2023] [Indexed: 02/02/2024]
Abstract
The third most prevalent malignancy to cause mortality is hepatocellular carcinoma (HCC). The Hedgehog (Hh) signaling pathway is activated by binding to the transmembrane receptor Patched-1 (PTCH-1), which depresses the transmembrane G protein-coupled receptor Smoothened (SMO). This study was performed to examine the preventative and therapeutic effects of cannabidiol in adult rats exposed to diethyl nitrosamine (DENA)-induced HCC.A total of 50 male rats were divided into five groups of 10 rats each. Group I was the control group. Group II received intraperitoneal (IP) injections of DENA for 14 weeks. Group III included rats that received cannabidiol (CBD) orally (3-30 mg/kg) for 2 weeks and DENA injections for 14 weeks. Group IV rats received oral CBD for 2 weeks before 14 weeks of DENA injections. Group V included rats that received CBD orally for 2 weeks after their last injection of DENA. Measurements were made for alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transferase (GGT), superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA), and alpha fetoprotein (AFP). Following total RNA extraction, Smo, Hhip, Ptch-1, and Gli-1 expressions were measured using quantitative real-time polymerase chain reaction (qRT-PCR). A histopathological analysis of liver tissues was performed.The liver enzymes, oxidant-antioxidant state, morphological, and molecular parameters of the adult male rat model of DENA-induced HCC showed a beneficial improvement after CBD administration. In conclusion, by focusing on the Hh signaling system, administration of CBD showed a beneficial improvement in the liver enzymes, oxidant-antioxidant status, morphological, and molecular parameters in the DENA-induced HCC in adult male rats.
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Affiliation(s)
- Samia Hussein
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Zagazig University, Zagazig, Egypt.
| | - Nabil A Soliman
- Department of Zoology, Faculty of Science, Zagazig University, Sharkia, Egypt
| | - Samih I El Dahmy
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Sharkia, Egypt
| | - Tarek Khamis
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt
| | - Reham Sameh
- Department of Pathology, Faculty of Medicine, Zagazig University, Sharkia, Egypt
| | - Fatma M Mostafa
- Department of Zoology, Faculty of Science, Zagazig University, Sharkia, Egypt
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Grimmelpont M, Payton L, Lefrançois C, Tran D. Molecular and behavioural responses of the mussel Mytilus edulis exposed to a marine heatwave. Mar Environ Res 2024; 196:106418. [PMID: 38402777 DOI: 10.1016/j.marenvres.2024.106418] [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: 12/28/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
Marine heatwaves (MHW) threaten marine organisms and tend to increase in frequency and intensity. We exposed the blue mussel Mytilus edulis to a MHW lasting 23 days, including two 10-d periods of thermal intensity increase of +5 °C (20 °C-25 °C) interspersed by 1 day back to 20 °C, followed by a 4-d recovery period. We investigated behaviour responses of mussels and gene expression changes relative to the circadian rhythm (Per), oxidative stress (SOD), cellular apoptosis (CASP3), energy production (ATPs), and general stress response (hsp70). Results showed that the MHW disturbed the valve activity of mussels. Particularly, mussels increased the number of valve micro-closures, showing a stressful state of organisms. Mussels also decreased Per, CASP3, ATPs, and Hsp70 gene expression. Some behavioural and molecular effects persisted after the MHW, suggesting a limited recovery capacity of individuals. This work highlighted the vulnerability of M. edulis to a realistic MHW.
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Affiliation(s)
- Margot Grimmelpont
- La Rochelle University/CNRS France - UMR7266 LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - Laura Payton
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33120, Arcachon, France
| | - Christel Lefrançois
- La Rochelle University/CNRS France - UMR7266 LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - Damien Tran
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33120, Arcachon, France.
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Lee HJ, Kim KT, Kim MS, Lee SY. Dataset for selection of stable reference genes for accurate quantitative gene expression analysis in silvertip tetra ( Hasemania nana): Implications for sex differentiation and determination. Data Brief 2024; 53:110221. [PMID: 38425875 PMCID: PMC10904181 DOI: 10.1016/j.dib.2024.110221] [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: 09/21/2023] [Revised: 01/18/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
Real-time quantitative PCR (RT-qPCR) is a widely used method for accurate quantitative gene expression analysis. For accurate quantitative verification of RT-qPCR, it is essential to select a reference gene with high expression stability depending on the experimental environment or the different tissues. In this study, we evaluated the stability of nine candidate reference genes, labeled elongation factor 1-alpha (EF1A), ERBB receptor feedback inhibitor 1-like isoform x2 (ERRFI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), integrin beta2 like (ITGB2), phosphatidylinositol-binding clathrin assembly protein-like isoform x3 (PICALM), 60 s ribosomal protein L5 (RPL5), 60 s ribosomal protein L7 (RPL7), tubulin beta chain (TUBB), and ubiquitin-conjugating enzyme E2A (UBE2A), in the brain (including pituitary gland) gonads and caudal fins of silvertip tetra (Hasemania nana) males and females. The stability evaluation of the reference gene was analyzed using a program based on the geNorm, NormFinder, BestKeeper, and RankAggreg algorithms. As a result, RPL5 (brain, caudal fin), EF1A (gonad), and PICALM (three tissue types) genes were evaluated as the most stable genes in silvertip tetra females. In males, TUBB (brain, caudal fin) and ITGB2 (gonads, three tissue types) genes were the most stable, and in both sexes, TUBB (brain), ITGB2 (caudal fin), RPL5 (gonads), and PICALM (three tissue types) genes are considered appropriate as reference genes for qRT-PCR analysis. However, the GAPDH gene was judged to be inappropriate for use as a reference gene because gene stability in the brain, caudal fin, and gonads was evaluated to be low in all males and females. As an introductory study on silvertip tetra, a new research model fish, the results of this study are expected to provide helpful information regarding sex differentiation and determination in fish.
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Affiliation(s)
- Hwa Jin Lee
- CellQua, Inc, Seongnam 13595, South Korea
- Department of Biological Sciences, Kongju National University, Gongju 32588, South Korea
| | - Ki Tae Kim
- Southeast Sea Fisheries Research Institute, NFRDI, 398-68, Sanyangilju-ro, Sangyang-Up Tongyeong, Gyoengnam 650-943, Korea
| | - Min Sun Kim
- Department of Biological Sciences, Kongju National University, Gongju 32588, South Korea
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Yang Y, Ma Q, Jin S, Huang B, Wang Z, Chen G. Identification of mapk genes, and their expression profiles in response to low salinity stress, in cobia (Rachycentron canadum). Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110950. [PMID: 38307403 DOI: 10.1016/j.cbpb.2024.110950] [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: 09/12/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
Mitogen-activated protein kinases (MAPKs) are a class of protein kinases that regulate various physiological processes, and play a crucial role in maintaining the osmotic equilibrium of fish. The objective of this study was to identify and characterize the mapk family genes in cobia (Rachycentron canadum) and examine their expression profiles under different low salinity stress regimes (acute: from 30‰ to 10‰ in 1 h, sub-chronic: from 30‰ to 10‰ over 4 d). A total of 12 cobia mapk genes (Rcmapks) were identified and cloned, including six erk subfamily genes (Rcmapk1/3/4/6/7/15), three jnk subfamily genes (Rcmapk8/9/10) and three p38 mapk subfamily genes (Rcmapk 11/13/14). Domain analysis indicated that the RcMAPKs possessed the typical domains including S_TKc and PKc_like domain. Phylogenetic analysis revealed that the Rcmapks were most closely related to those of the turbot (Scophthalmus maximus). The tissue distribution of mapk genes in adult cobia and the expression patterns of Rcmapks under different low salinity stress regimes were investigated using quantitative real-time PCR (qRT-PCR). The results revealed that Rcmapk3/9/10/11/13/14 exhibited a relatively broad expression distribution across 14 different tissues. For all these genes the highest expression level was in the brain, except for Rcmapk14 (highly expressed in the stomach, gill, and skin). The genes Rcmapk1/6/15 showed significantly higher expression in the testis. Under acute low salinity stress, expression of Rcmapk1/3/6/7/9/11/13/14 was significantly altered in the gill, intestine, and trunk kidney, however, the aforementioned genes exhibited very different expression patterns among the three tissues. In the gill, most of the genes from the erk (Rcmapk3/6/7) and p38 mapk subfamily (Rcmapk11/13/14) were significantly up-regulated at almost all the time points (P < 0.05); Similarly, the expression of Rcmapk3/9/11/13/14 genes were significantly increased in the trunk kidney; while in the intestine, most of the altered genes (Rcmapk6/7/9/11/13/14) were significantly down-regulated at 1 h. Following the sub-chronic low salinity stress, expression of Rcmapk1/3/6/7/9/11/13/14 genes were significantly altered in all three tissues. These findings provide important reference data for elucidating the roles of cobia mapk family genes in response to low salinity stress.
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Affiliation(s)
- Yunsheng Yang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qian Ma
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Shulei Jin
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Baosong Huang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhongliang Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Gang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
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Chao M, Huang L, Dong J, Chen Y, Hu G, Zhang Q, Zhang J, Wang Q. Molecular characterization and expression pattern of Rubisco activase gene GhRCAβ2 in upland cotton (Gossypium hirsutum L.). Genes Genomics 2024; 46:423-436. [PMID: 38324226 DOI: 10.1007/s13258-024-01494-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Rubisco activase (RCA) is a pivotal enzyme that can catalyse the activation of Rubisco in carbon assimilation pathway. Many studies have shown that RCA may be a potential target for genetic manipulation aimed at enhancing photosynthetic efficiency and crop yield. OBJECTIVE To understand the biological function of the GhRCAβ2 gene in upland cotton, we cloned the coding sequence (CDS) of the GhRCAβ2 gene and investigated its sequence features, evolutionary relationship, subcellular localization, promoter sequence and expression pattern. METHODS The bioinformatics tools were used to analyze the sequence features of GhRCAβ2 protein. Transient transformation of Arabidopsis mesophyll protoplasts was performed to determine the subcellular localization of the GhRCAβ2 protein. The expression pattern of the GhRCAβ2 gene was examined by analyzing transcriptome data and using the quantitative real-time PCR (qRT-PCR). RESULTS The full-length CDS of GhRCAβ2 was 1317 bp, and it encoded a protein with a chloroplast transit peptide. The GhRCAβ2 had two conserved ATP-binding domains, and did not have the C-terminal extension (CTE) domain that was unique to the RCA α-isoform in plants. Evolutionarily, GhRCAβ2 was clustered in Group A, and had a close evolutionary relationship with the soybean RCA. Western blot analysis demonstrated that GhRCAβ2 was immunoreactive to the RCA antibody displaying a molecular weight similar to that of the RCA β-isoform. The GhRCAβ2 protein was found in chloroplast, aligning with its role as a vital enzyme in the process of photosynthesis. The GhRCAβ2 gene had a leaf tissue-specific expression pattern, and the yellow-green leaf mutant exhibited a decreased expression of GhRCAβ2 in comparison to the wild-type cotton plants. The GhRCAβ2 promoter contained several cis-acting elements that respond to light, phytohormones and stress, suggesting that the expression of GhRCAβ2 may be regulated by these factors. An additional examination of stress response indicated that GhRCAβ2 expression was influenced by cold, heat, salt, and drought stress. Notably, diverse expression pattern was observed across different stress conditions. Additionally, low phosphorus and low potassium stress may result in a notable reduction in the expression of GhRCAβ2 gene. CONCLUSION Our findings will establish a basis for further understanding the function of the GhRCAβ2 gene, as well as providing valuable genetic knowledge to improve cotton photosynthetic efficiency and yield under challenging environmental circumstances.
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Affiliation(s)
- Maoni Chao
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ling Huang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jie Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Yu Chen
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Genhai Hu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Qiufang Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jinbao Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Qinglian Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, 453003, China.
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Appleby S, Aitken-Buck HM, Holdaway MS, Byers MS, Frampton CM, Paton LN, Richards AM, Lamberts RR, Pemberton CJ. Cardiac effects of myoregulin in ischemia-reperfusion. Peptides 2024; 174:171156. [PMID: 38246425 DOI: 10.1016/j.peptides.2024.171156] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Myoregulin is a recently discovered micropeptide that controls calcium levels by inhibiting the intracellular calcium pump sarco-endoplasmic reticulum Ca2+-ATPase (SERCA). Keeping calcium levels balanced in the heart is essential for normal heart functioning, thus myoregulin has the potential to be a crucial regulator of cardiac muscle performance by reducing the rate of intracellular Ca2+ uptake. We provide the first report of myoregulin mRNA expression in human heart tissue, absence of expression in human plasma, and the effects of myoregulin on cardiac hemodynamics in an ex vivo Langendorff isolated rat heart model of ischemia/reperfusion. In this preliminary study, myoregulin provided a cardio-protective effect, as assessed by preservation of left ventricular contractility and relaxation, during ischemia/reperfusion. This study provides the foundation for future research in this area.
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Affiliation(s)
- Sarah Appleby
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Hamish M Aitken-Buck
- Department of Physiology, HeartOtago, University of Otago, 270 Great King St, Dunedin 9016, New Zealand.
| | - Mark S Holdaway
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Mathew S Byers
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Chris M Frampton
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Louise N Paton
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - A Mark Richards
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand; Department of Cardiology, Te Whatu Ora Waitaha, 2 Riccarton Avenue, Christchurch 8011, New Zealand; Cardiovascular Research Institute, National University of Singapore, 1E Kent Ridge Road, Singapore.
| | - Regis R Lamberts
- Department of Physiology, HeartOtago, University of Otago, 270 Great King St, Dunedin 9016, New Zealand.
| | - Christopher J Pemberton
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
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Si S, Zhang X, Yu Y, Zhong X, Zhang X, Yuan J, Li F. Structure and function analyses of the SRC gene in Pacific white shrimp Litopenaeus vannamei. Fish Shellfish Immunol 2024; 147:109433. [PMID: 38336143 DOI: 10.1016/j.fsi.2024.109433] [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: 12/06/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
SRC gene encodes scavenger receptor class C, a member of the scavenger receptor family, and has only been identified and investigated in invertebrates. Our previous studies have revealed that SRC is a novel candidate gene associated with body weight in Pacific white shrimp (Litopenaeus vannamei). In order to comprehend the underlying mechanism by which LvSRC affects shrimp growth, we analyzed the structure, phylogeny, expression profiles and RNA interference (RNAi) of this gene in L. vannamei. We found that LvSRC contains two CCP domains and one MAM domain, with the highest expression level in the heart and relatively low expression level in other tissues. Notably, LvSRC exhibited significantly higher expression levels in the fast-growing group among groups with different growth rates, suggesting its potential involvement as a gene contributing to the growth of L. vannamei. RNAi of LvSRC inhibited body length and body weight gain compared to the control groups. Moreover, through RNA-seq analysis, we identified 598 differentially expressed genes (DEGs), including genes associated with growth, immunity, protein processing and modification, signal transduction, lipid synthesis and metabolism. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed significant changes in the signaling pathways related to growth, lipid metabolism and immune response, suggesting that LvSRC exhibits the potential to participate in diverse physiological processes and immune regulation. These findings deepen our understanding of the structure and function of the SRC in shrimp and lay the foundation for further research into the regulatory mechanism of LvSRC. Additionally, they provide potential applications in shrimp genetics and breeding.
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Affiliation(s)
- Shuqing Si
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaoyun Zhong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
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Zhao Y, Wang H, Xu Y, Wang K, Huang C, Deng Y, Huang J, Li Y. Characteristic analysis of BZR genes family and their responses to hormone treatments and abiotic stresses in Carya illinoinensis. Plant Sci 2024; 341:111990. [PMID: 38253206 DOI: 10.1016/j.plantsci.2024.111990] [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: 08/22/2023] [Revised: 12/04/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
As the core of Brassinosteroids (BR) signaling pathway, BR-resistant (BZR) transcription factor regulates thousands of targeted genes mediating photomophogenesis, pollen sterility, cell expansion and stress response. Pecan (Carya illinoinensis) is a famous trees species of Carya, and its nut has high nutritional and economic values. However, there has no report on BZR genes family in pecan yet. Herein, totals of seven CiBZR members were identified in pecan genome, which were predicted to be hydrophilic unstable proteins and located in the nucleus. CiBZR genes had close evolutionary relationships with CcBZRs and JrBZRs in both Carya cathayensis and Juglans regia. These seven CiBZR genes were located independently on 7 chromosomes without doubling or tandem duplication. Based on the analysis of conserved motifs and gene structures, CiBZR genes were divided into three categories. More than 40 cis-acting elements were found in the 2 kb promoter regions of CiBZRs, which were mainly involved in hormone, light, and stress response, and plant growth and development. Notably, some of these CiBZR proteins were mainly located in the nucleus, had the self-activation ability and interaction relationship with BIN2 kinase, and negatively regulated the expression of CiCPD and CiDWF4. Gene expressions analysis further showed that CiBZR genes could express in many tissues and shared similar expression trends during embryo development. Moreover, most CiBZR genes responded to BR, Gibberellin (GA), Strigolactone (SL), salt, acid and osmotic stress. This study provides theoretical basis for the subsequent study on the role of CiBZR family genes in plant growth, development and stress responses.
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Affiliation(s)
- Yirui Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Haoyu Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Yifan Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Chunying Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | | | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
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Dettleff P, Toloza C, Fuentes M, Aedo J, Zuloaga R, Estrada JM, Molina A, Valdés JA. Gills de novo assembly reveals oxidative stress, unfolded protein, and immune response on red cusk-eel (Genypterus chilensis) under thermal stress. Mar Environ Res 2024; 196:106440. [PMID: 38479297 DOI: 10.1016/j.marenvres.2024.106440] [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: 11/17/2023] [Revised: 02/18/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
The heat waves on the South Pacific coast could lead to thermal stress in native fish. The red cusk-eel (Genypterus chilensis) is relevant for Chilean artisanal fisheries and aquaculture diversification. This study examined the effect of high-temperature stress in the gills of G. chilensis in control (14 °C) and high-temperature stress (19 °C) conditions. High-temperature stress induces a significant increase in gills cortisol levels. Additionally, oxidative damage was observed in gills (protein carbonylation and lipoperoxidation). RNA-seq data was used to build the first transcriptome assembly of gills in this species (23,656 annotated transcripts). A total of 1138 down-regulated and 1531 up-regulated transcripts were observed in response to high-temperature stress in gills. The enrichment analysis showed immune response and replication enriched processes (on down-regulated transcripts), and processes related to the folding of proteins, endoplasmic reticulum, and transporter activity (on up-regulated transcripts). The present study showed how gills could be affected by high-temperature stress.
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Affiliation(s)
- Phillip Dettleff
- Escuela de Medicina Veterinaria, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile.
| | - Carla Toloza
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile
| | - Marcia Fuentes
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile
| | - Jorge Aedo
- Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, 3466706, Chile
| | - Rodrigo Zuloaga
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile
| | - Juan Manuel Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, 2340000, Chile
| | - Alfredo Molina
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile
| | - Juan Antonio Valdés
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile.
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Batista RITP, Dias JH, Gonçalves JD, Vergani GB, Oliveira MEF, Souza-Fabjan JMG, Fonseca JF. The presence of estradiol benzoate in the cervical relaxation treatment for non-surgical embryo collection does not impair embryonic morphological quality, cryosurvival, and gene expression profile. Theriogenology 2024; 218:208-213. [PMID: 38335708 DOI: 10.1016/j.theriogenology.2024.01.038] [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: 10/20/2023] [Revised: 01/08/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
Non-surgical embryo recovery (NSER) is usually preceded by a cervical relaxation in ovine donors, based on estradiol benzoate (EB), prostaglandin (PGF), and oxytocin (OT). However, it is hypothesized that, due to poorly understood mechanisms, EB can result in embryotoxic actions. To evaluate this, 20 min before NSER superovulated sheep were induced to cervical relaxation with 0.0 (G0.0), 0.5 (G0.5), or 1.0 mg (G1.0) of EB associated with 37.5 μg of PGF 16 h before NSER and 50 IU of OT. In doing so, the efficiency and duration of the NSER procedure showed no compromise (P > 0.05). Additionally, the presence of EB did not affect (P > 0.05) the embryo's morphological quality, the development dynamics, or the abundance of transcripts associated with embryonic quality (OCT4 and NANOG), cellular stress (HSP90 and PRDX1), and apoptosis (BCL2 and BAX). A similar result (P > 0.05) was also observed when comparing embryonic cryosurvival at 24 (52.0, 52.0, and 54.0) and 48 h (60.0, 54.0, and 58.0) of in vitro culture (G0.0, G0.5, and G1.0, respectively). Thus, we can conclude that EB use does not compromise embryonic quality and cryoresistance.
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Affiliation(s)
| | | | - Joedson Dantas Gonçalves
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Gabriel Brun Vergani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Maria Emilia Franco Oliveira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/n, 14884-900, Jaboticabal, SP, Brazil
| | | | - Jeferson Ferreira Fonseca
- Embrapa Caprinos e Ovinos, Núcleo Regional Sudeste, Rodovia MG 133, Km 42, CEP 36155 - 000, Coronel Pacheco, MG, Brazil
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Jung YS, Radhakrishnan K, Kim HJ, Kim YH, Lee CH, Choi HS. Macrophage stimulating protein is a novel transcriptional target of estrogen related receptor gamma in alcohol-intoxicated mice. Cell Signal 2024; 116:111059. [PMID: 38237793 DOI: 10.1016/j.cellsig.2024.111059] [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: 09/12/2023] [Revised: 12/27/2023] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
Macrophage stimulating protein (MSP) is a multifunctional serum protein produced in the liver, belonging to the plasminogen-related kringle protein family. It exerts diverse biological functions by activating a transmembrane receptor protein-tyrosine kinase known as RON in humans and SKT in mice. MSP plays a pivotal role in innate immunity and is involved in various activities such as cell survival, migration, and phagocytosis. Elucidating the regulatory mechanisms governing MSP gene expression is of great importance. In this study, we comprehensively elucidate the molecular mechanism underlying hepatic MSP gene expression in response to alcoholism. Exposure to ethanol specifically upregulated the expression of ERRγ and MSP in the liver, while not in other organs. Liver-specific knockout of the cannabinoid receptor type 1 (CB1R), an upstream regulator of ERRγ, inhibited the alcohol-induced upregulation of MSP expression. Overexpression of ERRγ alone was sufficient to enhance MSP expression in hepatic cell lines and in mice. Conversely, knockdown of ERRγ in cell lines or liver-specific knockout of ERRγ in mice reversed ethanol-induced MSP gene expression. Promoter studies revealed the direct binding of ERRγ to the MSP gene promoter at the ERR response element (ERRE), resulting in the positive regulation of MSP gene expression in response to alcohol. This finding was further supported by ERRE-mutated MSP-luciferase reporter assays. Notably, treatment with GSK5182, an ERRγ-specific inverse agonist, significantly suppressed alcohol-induced hepatic MSP expression. Collectively, we exposed a novel mechanistic understanding of how alcohol-induced ERRγ controls the transcriptional regulation of MSP gene expression in the liver.
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Affiliation(s)
- Yoon Seok Jung
- Host-Directed Antiviral Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kamalakannan Radhakrishnan
- Host-Directed Antiviral Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyo-Jin Kim
- Host-Directed Antiviral Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yong-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hueng-Sik Choi
- Host-Directed Antiviral Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.
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Zheng X, Qiu L, Huang Y, Cheng R, Huang S, Xu K, Cai W, Deng Y, Wang W, Zhong X, Cui F, Hao Z, Liu J. Exploring the molecular and immune-landscape of lung cancer associated with cystic airspaces. Mol Immunol 2024; 168:75-88. [PMID: 38430689 DOI: 10.1016/j.molimm.2024.01.007] [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: 10/31/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024]
Abstract
To explore the molecular biological characteristics of lung cancer associated with cystic airspaces (LCCA) and its potential roles on prognosis. A total of 165 LCCAs and 201 non-LCCAs were enrolled in this study. Bulk RNA sequencing was implemented in eight LCCAs and nine non-LCCAs to explore the differentially expressed genes. TCGA data were used to analyze LCCA-specific genes that associated with overall survival (OS). The median age was 60 (IQR 53 to 65) years in LCCA cohort. We found LCCA were predominant in men and had less visceral pleura invasion (VPI) or lympho-vascular invasion (LVI). Moreover, LCCA presented with higher histological heterogeneity. Kaplan-Meier analysis showed that patients of age more than 60 and positive VPI had significantly less PFS in LCCA. Cox regression suggested that LCCA, micropapillary subtype proportion and VPI were the independent risk factors for PFS. LCCA had up-regulated pathways associated with EMT, angiogenesis and cell migration. In addition, LCCA displayed higher levels of immunosuppressor infiltration (M2 macrophages, CAFs and MDSCs) and distinct cell death and metabolic patterns. BCR/TCR repertoire analysis revealed less BCR richness, clonality and high-abundance shared clonotypes in LCCA. Finally, Cox regression analysis identified that four cystic-specific genes, KCNK3, NRN1, PARVB and TRHDE-AS1, were associated with OS of lung adenocarcinoma (LUAD). And cystic-specific risk scores (CSRSs) were calculated to construct a nomogram, which performance well. Our study for the first time indicated significantly distinct molecular biological and immune characteristics between LCCA and non-LCCA, which provide complementary prognostic values in early-stage non-small cell lung cancer (NSCLC).
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Affiliation(s)
- Xiang Zheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China; Department of Oncology, The First Clinical Medical College of Henan University, Kaifeng, China
| | - Li Qiu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ying Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ran Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Sihe Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ke Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weipeng Cai
- Department of Thoracic Surgery, Shantou Central Hospital, Shantou, China
| | - Yu Deng
- Department of Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Xi Zhong
- Department of Medical Imaging, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Fei Cui
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhexue Hao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China.
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Soliman NA, El Dahmy SI, Khamis T, Sameh R, Alashqar SM, Hussein S. The potential protective and therapeutic effects of cannabidiol oil on experimental Leukemia induced by DMBA in male rats. Naunyn Schmiedebergs Arch Pharmacol 2024; 397:2389-2400. [PMID: 37837474 DOI: 10.1007/s00210-023-02737-6] [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: 07/29/2023] [Accepted: 09/20/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND 7,12-Dimethylbenzanthracene (DMBA) is a member of the polycyclic aromatic hydrocarbon family. It is a member of the polycyclic aromatic hydrocarbon family. It is a mutagenic, carcinogenic, and immunosuppressor agent. Cannabidiol (CBD) is a phytocannabinoid. It has anticonvulsant, anti-inflammatory, anti-anxiety, antioxidant, and anti-cancer properties. The purpose of this study was to investigate the possible protective and therapeutic benefits of CBD oil in DMBA-induced leukemia in rats. METHOD Experimental animals were divided into six groups of five rats each. Group 1 (normal control) included healthy rats. Group 2 included normal rats that received olive oil. Group 3 included normal rats that received CBD. Group 4 included the DMBA-induced leukemic group. Group 5 (prophylactic group) included rats that received CBD as a prophylaxis before IV injection with DMBA. Group 6 (treated group) included DMBA-induced leukemic rats that received CBD as treatment. Liver functions (total, direct and indirect bilirubin, alkaline phosphatase (ALP), alanine transaminase (ALT), aspartate aminotransferase (AST), albumin, globulin, and albumin globulin ratio) were measured. Superoxide dismutase (SOD) and catalase (CAT) were also measured. Total RNA extraction followed by-real time qRT-PCR gene expression of LC3-II, Beclin, mTOR, and P62 was performed. Histopathological examination of liver and spleen tissues was performed. RESULTS Administration of CBD in groups 5 and 6 resulted in a significant improvement of the levels of liver functions compared to the leukemic untreated rats. Also, the levels of catalase and SOD significantly increased after treatment with CBD compared to the leukemic group. After treatment with CBD in groups 5 and 6, there were downregulations in the expression of all studied genes compared to leukemic untreated rats. Treatment with CBD was more statistically effective than prophylactic use. CONCLUSION Administration of CBD resulted in a significant improvement in the biochemical, antioxidant status, morphological, and molecular measures in DMBA-induced leukemia in adult male rats. The therapeutic use was more effective than the prophylactic one.
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Affiliation(s)
- Nabil A Soliman
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Samih I El Dahmy
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Tarek Khamis
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Reham Sameh
- Department of Pathology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | | | - Samia Hussein
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Zagazig University, Zagazig, Egypt.
- Department of Basic Medical Sciences, Ibn Sina University for Medical Sciences, Amman, Jordan.
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Hrabak M, Moon C, Bolaños-Guzmán CA, Steiner H. Vilazodone, a Selective Serotonin Reuptake Inhibitor with Diminished Impact on Methylphenidate-Induced Gene Regulation in the Striatum: Role of 5-HT1A Receptor. Mol Neurobiol 2024; 61:1907-1919. [PMID: 37807008 DOI: 10.1007/s12035-023-03688-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
Selective serotonin reuptake inhibitors (SSRIs), including fluoxetine, are frequently combined with medical psychostimulants such as methylphenidate (Ritalin), for example, in the treatment of attention-deficit hyperactivity disorder/depression comorbidity. Co-exposure to these medications also occurs with misuse of methylphenidate as a recreational drug by patients on SSRIs. Methylphenidate, a dopamine reuptake blocker, produces moderate addiction-related gene regulation. Findings show that SSRIs such as fluoxetine given in conjunction with methylphenidate potentiate methylphenidate-induced gene regulation in the striatum in rats, consistent with a facilitatory action of serotonin on addiction-related processes. These SSRIs may thus increase methylphenidate's addiction liability. Here, we investigated the effects of a novel SSRI, vilazodone, on methylphenidate-induced gene regulation. Vilazodone differs from prototypical SSRIs in that, in addition to blocking serotonin reuptake, it acts as a partial agonist at the 5-HT1A serotonin receptor subtype. Studies showed that stimulation of the 5-HT1A receptor tempers serotonin input to the striatum. We compared the effects of acute treatment with vilazodone (10-20 mg/kg) with those of fluoxetine (5 mg/kg) on striatal gene regulation (zif268, substance P, enkephalin) induced by methylphenidate (5 mg/kg), by in situ hybridization histochemistry combined with autoradiography. We also assessed the impact of blocking 5-HT1A receptors by the selective antagonist WAY-100635 (0.5 mg/kg) on these responses. Behavioral effects of these drug treatments were examined in parallel in an open-field test. Our results show that, in contrast to fluoxetine, vilazodone did not potentiate gene regulation induced by methylphenidate in the striatum, while vilazodone enhanced methylphenidate-induced locomotor activity. However, blocking 5-HT1A receptors by WAY-100635 unmasked a potentiating effect of vilazodone on methylphenidate-induced gene regulation, thus confirming an inhibitory role for 5-HT1A receptors. Our findings suggest that vilazodone may serve as an adjunct SSRI with diminished addiction facilitating properties and identify the 5-HT1A receptor as a potential therapeutic target to treat addiction.
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Affiliation(s)
- Michael Hrabak
- Stanson Toshok Center for Brain Function and Repair, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
| | - Connor Moon
- Stanson Toshok Center for Brain Function and Repair, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
| | - Carlos A Bolaños-Guzmán
- Department of Psychological and Brain Sciences, Institute for Neuroscience, Texas A&M University, College Station, TX, 77843, USA
| | - Heinz Steiner
- Stanson Toshok Center for Brain Function and Repair, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
- Discipline of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
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Cai M, Ji Y, Zhao Q, Xue H, Sun Z, Wang H, Zhang Y, Chen Y, Zhao Y, Zhang Y, Lei M, Wang C, Zhuo C, Liu N, Liu H, Liu F. Homotopic functional connectivity disruptions in schizophrenia and their associated gene expression. Neuroimage 2024; 289:120551. [PMID: 38382862 DOI: 10.1016/j.neuroimage.2024.120551] [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: 12/11/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/23/2024] Open
Abstract
It has been revealed that abnormal voxel-mirrored homotopic connectivity (VMHC) is present in patients with schizophrenia, yet there are inconsistencies in the relevant findings. Moreover, little is known about their association with brain gene expression profiles. In this study, transcription-neuroimaging association analyses using gene expression data from Allen Human Brain Atlas and case-control VMHC differences from both the discovery (meta-analysis, including 9 studies with a total of 386 patients and 357 controls) and replication (separate group-level comparisons within two datasets, including a total of 258 patients and 287 controls) phases were performed to identify genes associated with VMHC alterations. Enrichment analyses were conducted to characterize the biological functions and specific expression of identified genes, and Neurosynth decoding analysis was performed to examine the correlation between cognitive-related processes and VMHC alterations in schizophrenia. In the discovery and replication phases, patients with schizophrenia exhibited consistent VMHC changes compared to controls, which were correlated with a series of cognitive-related processes; meta-regression analysis revealed that illness duration was negatively correlated with VMHC abnormalities in the cerebellum and postcentral/precentral gyrus. The abnormal VMHC patterns were stably correlated with 1287 genes enriched for fundamental biological processes like regulation of cell communication, nervous system development, and cell communication. In addition, these genes were overexpressed in astrocytes and immune cells, enriched in extensive cortical regions and wide developmental time windows. The present findings may contribute to a more comprehensive understanding of the molecular mechanisms underlying VMHC alterations in patients with schizophrenia.
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Affiliation(s)
- Mengjing Cai
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yuan Ji
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiyu Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hui Xue
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zuhao Sun
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - He Wang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yijing Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yayuan Chen
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yao Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yujie Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Minghuan Lei
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chunyang Wang
- Department of Scientific Research, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chuanjun Zhuo
- Laboratory of Psychiatric-Neuroimaging-Genetic and Co-morbidity (PGNP_Lab), Tianjin Anding Hospital, Nankai University Affiliated Tianjin Anding Hospital, Tianjin Mental Health Center of Tianjin Medical University, Tianjin, 300222, China
| | - Nana Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Huaigui Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Feng Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
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Pal S, Paladhi P, Dutta S, Mullick RB, Bose G, Ghosh P, Chattopadhyay R, Ghosh S. Novel Mutations Reduce Expression of Meiotic Regulators SYCE1 and BOLL in Testis of Azoospermic Men from West Bengal, India. Reprod Sci 2024; 31:1069-1088. [PMID: 37957469 DOI: 10.1007/s43032-023-01393-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
We investigated the polymorphisms/mutations in synaptonemal complex central element protein 1 (SYCE1) and CDC25A mRNA-binding protein (BOLL) to test whether they increase the risk of azoospermia among Bengali-speaking men from West Bengal, India. Sanger's dideoxy sequencing was used to genotype 140 azoospermic individuals who tested negative for Y chromosome microdeletion and 120 healthy controls. In both cases and controls, qRT-PCR was used to determine the expression summary of SYCE1 and BOLL. The perceived harmful consequences of identified mutations were inferred using in silico analysis. Suitable statistical approaches were used to conduct the association study. We found SYCE1 177insT (ON245141), 10650T > G (ON257012), 10093insT (ON257013), 10653insG (ON292504), rs10857748A > G, rs10857749G > A, and rs10857750T > A and BOLL 7708T > A (ON245141insT), rs72918816T > C, and rs700655C > T variants with the prevalence of azoospermia. Data from qRT-PCR and in silico studies projected that the variations would either disrupt the transcript's natural splice junctions or cause probable damage to the structure of the genes' proteins. SYCE1 gene variants [177insT (ON245141), 10650T > G (ON257012), 10093insT (ON257013), 10653insG (ON292504), rs10857748A > G, rs10857749G > A, rs10857750T > A] and BOLL gene variants [7708T > A (ON245141insT), rs72918816T > C, rs700655C > T] reduce the expression of respective gene in testicular tissue among azoospermic male as revealed from qRT-PCR result. These genetic variations could be utilized as screening tools for male infertility to determine the best course of treatment in routine ART practise.
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Affiliation(s)
- Samudra Pal
- Cytogenetics & Genomics Research Unit, Department of Zoology, University of Calcutta, Taraknath-Palit-Siksha-Prangan, Ballygunge Science College Campus, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Pranab Paladhi
- Cytogenetics & Genomics Research Unit, Department of Zoology, University of Calcutta, Taraknath-Palit-Siksha-Prangan, Ballygunge Science College Campus, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Saurav Dutta
- Cytogenetics & Genomics Research Unit, Department of Zoology, University of Calcutta, Taraknath-Palit-Siksha-Prangan, Ballygunge Science College Campus, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Rupam Basu Mullick
- Cytogenetics & Genomics Research Unit, Department of Zoology, University of Calcutta, Taraknath-Palit-Siksha-Prangan, Ballygunge Science College Campus, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Gunja Bose
- Institute of Reproductive Medicine (IRM), HB-36/A/3 1St Cross Rd Bidhannagar, Sector III, Bidhannagar, Kolkata, West Bengal, 700106, India
| | - Papiya Ghosh
- Department of Zoology, Bijoy Krishna Girls' College Affiliated to University of Calcutta), Howrah, West Bengal, India
| | - Ratna Chattopadhyay
- Institute of Reproductive Medicine (IRM), HB-36/A/3 1St Cross Rd Bidhannagar, Sector III, Bidhannagar, Kolkata, West Bengal, 700106, India
| | - Sujay Ghosh
- Cytogenetics & Genomics Research Unit, Department of Zoology, University of Calcutta, Taraknath-Palit-Siksha-Prangan, Ballygunge Science College Campus, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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Binjawhar DN, Al-Enazi NM, Alsamhary K, Kha M. Plant mediated biosynthesis of Mn 3O 4 nanostructures and their biomedical applications. Heliyon 2024; 10:e27695. [PMID: 38509884 PMCID: PMC10951605 DOI: 10.1016/j.heliyon.2024.e27695] [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: 07/21/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Nanomaterials have drawn significant attention for their biomedical and pharmaceutical applications. In the present study, manganese tetra oxide (Mn3O4) nanoparticles were prepared greenly, and their physicochemical properties were studied. Taxus baccata acetone extract was used as a safely novel precursor for reducing and stabilizing nanoparticles. The synthesized nanoparticles were characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), Brunauer-Emmett-Teller (BET), and Barrett-Joyner-Halenda (BJH) and X-ray diffraction (XRD). The cytotoxicity of Mn3O4 (hausmannite) nanostructures was evaluated against murine macrophage cell line J774-A1 and U87 glioblastoma cancer cells for approximately 72 h. Spherical Mn3O4 nanoparticles with tetragonal spinel structures demonstrated minimal toxicity against normal body cells with CC50 around 876.38 μg mL-1. Moreover, Mn3O4 nanoparticles as well as the combination of antimoniate meglumine and Mn3O4 nanoparticles exhibited maximum mortality in Leishmania major. The synthesized nanominerals displayed a significant inhibitory effect against glioblastoma cancer cells at 100 μg mL-1. The selective cytotoxicity of Mn3O4 nanoparticles indicates that these biogenic agents can be employed simultaneously for diagnostic and therapeutic applications in medical applications.
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Affiliation(s)
- Dalal N. Binjawhar
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Nouf M. Al-Enazi
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Khawla Alsamhary
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Mansour Kha
- Antibacterial Materials R&D Centre, Huzhou Institute, Huzhou, Zhejiang, China
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Naseema Rasheed R, Suhara Beevy S. Reliable reference gene selection for quantitative real-time PCR (qRT-PCR) in floral developmental phases of dioecious species Coccinia grandis. Gene 2024; 900:148143. [PMID: 38195051 DOI: 10.1016/j.gene.2024.148143] [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: 10/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
The flowering process is intricate and regulated by a combination of external and internal factors. Delving into gene expression research has the potential to enhance our comprehension of the molecular foundations underlying floral development. Because of its accuracy, specificity, reproducibility, and efficiency, qRT-PCR is now a biological research tool for studying expression pattern of desired genes. The gene expression investigations using qRT-PCR required a reference gene with relatively uniform expression levels in multiple biological samples, including different developmental stages, tissues, and experimental conditions. In this study, experimental sets offloral and floral organ development in the male and female plants of C. grandis, a dioecious Cucurbitaceae species, qRT-PCR profiling was performed using six reference genes as internal control with B-class floral identity gene, PISTILLATA (PI). To analyse the data, algorithms such as geNorm, NormFinder, RefFinder, and BestKeeper were used to pick out the best internal controls from a group of candidates. The optimal reference gene for qRT-PCR studies with floral samples has been recommended as β-actin combined with β-tubulin. This is the first report on the validation of candidate reference genes across flower developmental stages in the dioecious species C. grandis, which will provide basic data for research on the molecular mechanism underlying flower development in this species and lay the groundwork for similar studies in other related species.
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Affiliation(s)
| | - S Suhara Beevy
- Department of Botany, University of Kerala, Kariavattom Campus, Kerala, India
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Mohamed DA, Fouda K, Mabrok HB, El-Shamarka ME, Hamed IM. Sourdough bread as nutritional intervention tool for improvement of cognitive dysfunction in diabetic rats. BMC Nutr 2024; 10:53. [PMID: 38528644 DOI: 10.1186/s40795-024-00861-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The current research targeted to study the impact of nutritional intervention by two sourdough breads in improvement of cognitive dysfunction in diabetic rats. METHODS Type-2 diabetes was induced in rats by Streptozotocin-Nicotinamide (STZ-NC). Diabetic rats were fed on balanced diet or balanced diet containing 20% of sourdough bread I or II for a month. Lipid profile, oxidative stress, inflammatory markers and cognitive functions were assessed in all rats. Gene expression of brain-derived neurotrophic factor (BDNF) and nuclear respiratory factor 2 (NRF-2) were assessed in hippocampal tissue, while expression of phosphoenol pyruvate carboxy kinase (PEPCK), and glucose transporter 2 (GLUT2) genes were evaluated in hepatic tissue. Chemical composition and fatty acids profile were evaluated in the prepared sourdough bread. RESULTS Sourdough bread II showed higher content of phenolic compounds, fat, fiber and carbohydrates. Fatty acids profile revealed that sourdough bread I was higher in saturated fatty acids (16.08%), while sourdough bread sample II was higher in unsaturated fatty acids (79.33%). Sourdough bread I or II feeding rats' showed significant improvement in hyperglycemia, oxidative stress markers, inflammatory markers, lipid profile, liver and kidney functions in association with improvement in cognitive function. Gene expression of BDNF and NRF2 in hippocampal tissue were increased significantly, while hepatic GLUT2 and PEPCK gene expression were down-regulated in diabetic given sourdough bread I or II. CONCLUSION Sourdough bread II was superior in all the studied parameters. The anti-diabetic effect and protection from cognitive dysfunction of sourdough bread samples may be ascribed to the occurrence of dietary fibers, phenolic compounds, and polyunsaturated fatty acids.
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Affiliation(s)
- Doha A Mohamed
- Nutrition and Food Science Department, Food Industries and Nutrition Institute, National Research Centre, Dokki, Cairo, 12622, Egypt.
| | - Karem Fouda
- Nutrition and Food Science Department, Food Industries and Nutrition Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Hoda B Mabrok
- Nutrition and Food Science Department, Food Industries and Nutrition Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Marwa E El-Shamarka
- Toxicology and Narcotics Department, Medical Research and Clinical Studies Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Ibrahim M Hamed
- Nutrition and Food Science Department, Food Industries and Nutrition Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
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Jiao Y, Tan J, Guo H, Huang B, Ying Y, Ramakrishnan M, Zhang Z. Genome-wide analysis of the KNOX gene family in Moso bamboo: insights into their role in promoting the rapid shoot growth. BMC Plant Biol 2024; 24:213. [PMID: 38528453 DOI: 10.1186/s12870-024-04883-2] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND KNOTTED1-like homeobox (KNOX) genes, plant-specific homologous box transcription factors (TFs), play a central role in regulating plant growth, development, organ formation, and response to biotic and abiotic stresses. However, a comprehensive genome-wide identification of the KNOX genes in Moso bamboo (Phyllostachys edulis), the fastest growing plant, has not yet been conducted, and the specific biological functions of this family remain unknown. RESULTS The expression profiles of 24 KNOX genes, divided into two subfamilies, were determined by integrating Moso bamboo genome and its transcriptional data. The KNOX gene promoters were found to contain several light and stress-related cis-acting elements. Synteny analysis revealed stronger similarity with rice KNOX genes than with Arabidopsis KNOX genes. Additionally, several conserved structural domains and motifs were identified in the KNOX proteins. The expansion of the KNOX gene family was primarily regulated by tandem duplications. Furthermore, the KNOX genes were responsive to naphthaleneacetic acid (NAA) and gibberellin (GA) hormones, exhibiting distinct temporal expression patterns in four different organs of Moso bamboo. Short Time-series Expression Miner (STEM) analysis and quantitative real-time PCR (qRT-PCR) assays demonstrated that PeKNOX genes may play a role in promoting rapid shoot growth. Additionally, Gene Ontology (GO) and Protein-Protein Interaction (PPI) network enrichment analyses revealed several functional annotations for PeKNOXs. By regulating downstream target genes, PeKNOXs are involved in the synthesis of AUX /IAA, ultimately affecting cell division and elongation. CONCLUSIONS In the present study, we identified and characterized a total of 24 KNOX genes in Moso bamboo and investigated their physiological properties and conserved structural domains. To understand their functional roles, we conducted an analysis of gene expression profiles using STEM and RNA-seq data. This analysis successfully revealed regulatory networks of the KNOX genes, involving both upstream and downstream genes. Furthermore, the KNOX genes are involved in the AUX/IAA metabolic pathway, which accelerates shoot growth by influencing downstream target genes. These results provide a theoretical foundation for studying the molecular mechanisms underlying the rapid growth and establish the groundwork for future research into the functions and transcriptional regulatory networks of the KNOX gene family.
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Affiliation(s)
- Yang Jiao
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jiaqi Tan
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Hui Guo
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Bin Huang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yeqing Ying
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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Groiss S, Viertler C, Kap M, Bernhardt G, Mischinger HJ, Sieuwerts A, Verhoef C, Riegman P, Kruhøffer M, Svec D, Sjöback SR, Becker KF, Zatloukal K. Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome: Implications for research and diagnostics. N Biotechnol 2024; 79:20-29. [PMID: 38072306 DOI: 10.1016/j.nbt.2023.12.001] [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: 09/14/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Cellular responses induced by surgical procedure or ischemia-reperfusion injury (IRI) may severely alter transcriptome profiles and complicate molecular diagnostics. To investigate this effect, we characterized such pre-analytical effects in 143 non-malignant liver samples obtained from 30 patients at different time points of ischemia during surgery from two individual cohorts treated either with the Pringle manoeuvre or total vascular exclusion. Transcriptomics profiles were analyzed by Affymetrix microarrays and expression of selected mRNAs was validated by RT-PCR. We found 179 mutually deregulated genes which point to elevated cytokine signaling with NFκB as a dominant pathway in ischemia responses. In contrast to ischemia, reperfusion induced pro-apoptotic and pro-inflammatory cascades involving TNF, NFκB and MAPK pathways. FOS and JUN were down-regulated in steatosis compared to their up-regulation in normal livers. Surprisingly, molecular signatures of underlying primary and secondary cancers were present in non-tumor tissue. The reported inter-patient variability might reflect differences in individual stress responses and impact of underlying disease conditions. Furthermore, we provide a set of 230 pre-analytically highly robust genes identified from histologically normal livers (<2% covariation across both cohorts) that might serve as reference genes and could be particularly suited for future diagnostic applications.
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Affiliation(s)
- Silvia Groiss
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Christian Viertler
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Marcel Kap
- Pathology Department, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Gerwin Bernhardt
- Division of General Surgery, Department of Surgery, Medical University of Graz, 8010 Graz, Austria; Department of Orthopedics and Trauma Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Hans-Jörg Mischinger
- Division of General Surgery, Department of Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Anieta Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Cees Verhoef
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Peter Riegman
- Pathology Department, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | | | - David Svec
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic
| | | | | | - Kurt Zatloukal
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.
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Isa V, Seveso D, Diamante L, Montalbetti E, Montano S, Gobbato J, Lavorano S, Galli P, Louis YD. Physical and cellular impact of environmentally relevant microplastic exposure on thermally challenged Pocillopora damicornis (Cnidaria, Scleractinia). Sci Total Environ 2024; 918:170651. [PMID: 38320710 DOI: 10.1016/j.scitotenv.2024.170651] [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: 10/11/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Microplastic pollution is an increasing threat to coral reefs, which are already strongly challenged by climate change-related heat stress. Although it is known that scleractinian corals can ingest microplastic, little is known about their egestion and how microplastic exposure may impair corals at physiological and cellular levels. In addition, the effects of microplastic pollution at current environmental concentration have been little investigated to date, particularly in corals already impacted by heat stress. In this study, the combined effects of these environmental threats on Pocillopora damicornis were investigated from a physical and cellular perspective. Colonies were exposed to three concentrations of polyethylene microplastic beads (no microplastic beads: [No MP], 1 mg/L: [Low MP]; 10 mg/L: [High MP]), and two different temperatures (25 °C and 30 °C) for 72 h. No visual signs of stress in corals, such as abnormal mucus production and polyp extroflection, were recorded. At [Low MP], beads adhered to colonies were ingested but were also egested. Moreover, thermally stressed colonies showed a lower adhesion and higher egestion of microplastic beads. Coral bleaching was observed with an increase in temperature and microplastic bead concentration, as indicated by a general decrease in chlorophyll concentration and Symbiodiniaceae density. An increase in lipid peroxidation was measured in colonies exposed to [Low MP] and [High MP] and an up-regulation of stress response gene hsp70 was observed due to the synergistic interaction of both stressors. Overall, our findings showed that heat stress still represents the main threat to P. damicornis, while the effect of microplastics on coral health and physiology may be minor, especially at control temperature. However, microplastics could exacerbate the effect of thermal stress on cellular homeostasis, even at [Low MP]. While reducing ocean warming is critical for preserving coral reefs, effective management of emerging threats like microplastic pollution is equally essential.
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Affiliation(s)
- Valerio Isa
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives; Costa Edutainment SpA - Acquario di Genova, Area Porto Antico, Ponte Spinola, 16128 Genoa, Italy
| | - Davide Seveso
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives
| | - Luca Diamante
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Enrico Montalbetti
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives.
| | - Simone Montano
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives
| | - Jacopo Gobbato
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives
| | - Silvia Lavorano
- Costa Edutainment SpA - Acquario di Genova, Area Porto Antico, Ponte Spinola, 16128 Genoa, Italy
| | - Paolo Galli
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives; University of Dubai, Dubai, P.O. Box 14143, United Arab Emirates
| | - Yohan Didier Louis
- Department of Earth and Environmental Science, University of Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; MaRHE Center (Marine Research and High Education Center), Magoodhoo Island, Faafu Atoll, Maldives
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Huang F, Li Z, Yang X, Liu H, Chen L, Chang N, He H, Zeng Y, Qiu T, Fang L. Silicon reduces toxicity and accumulation of arsenic and cadmium in cereal crops: A meta-analysis, mechanism, and perspective study. Sci Total Environ 2024; 918:170663. [PMID: 38311087 DOI: 10.1016/j.scitotenv.2024.170663] [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: 12/12/2023] [Revised: 01/20/2024] [Accepted: 02/01/2024] [Indexed: 02/06/2024]
Abstract
Arsenic (As) and cadmium (Cd) are two toxic metal(loid)s that pose significant risks to food security and human health. Silicon (Si) has attracted substantial attention because of its positive effects on alleviating the toxicity and accumulation of As and Cd in crops. However, our current knowledge of the comprehensive effects and detailed mechanisms of Si amendment is limited. In this study, a global meta-analysis of 248 original articles with over 7000 paired observations was conducted to evaluate Si-mediated effects on growth and As and Cd accumulation in rice (Oryza sativa L.), wheat (Triticum aestivum L.), and maize (Zea mays L.). Si application increases the biomass of these crops under As and/or Cd contamination. Si amendment also decreased shoot As and Cd accumulation by 24.1 % (20.6 to 27.5 %) and 31.9 % (29.0 to 31.9 %), respectively. Furthermore, the Si amendment reduced the human health risks posed by As (2.6 %) and Cd (12.9 %) in crop grains. Si-induced inhibition of Cd accumulation is associated with decreased Cd bioavailability and the downregulation of gene expression. The regulation of gene expression by Si addition was the driving factor limiting shoot As accumulation. Overall, our analysis demonstrated that Si amendment has great potential to reduce the toxicity and accumulation of As and/or Cd in crops, providing a scientific basis for promoting food safety globally.
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Affiliation(s)
- Fengyu Huang
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zimin Li
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710061, China
| | - Xing Yang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China
| | - Hongjie Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Chen
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Nan Chang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Zeng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianyi Qiu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linchuan Fang
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
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