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Vidović A, Dolinar K, Chibalin AV, Pirkmajer S. AMPK and glucose deprivation exert an isoform-specific effect on the expression of Na +,K +-ATPase subunits in cultured myotubes. J Muscle Res Cell Motil 2024; 45:139-154. [PMID: 38709429 DOI: 10.1007/s10974-024-09673-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
In skeletal muscle, Na+,K+-ATPase (NKA), a heterodimeric (α/β) P-type ATPase, has an essential role in maintenance of Na+ and K+ homeostasis, excitability, and contractility. AMP-activated protein kinase (AMPK), an energy sensor, increases the membrane abundance and activity of NKA in L6 myotubes, but its potential role in regulation of NKA content in skeletal muscle, which determines maximum capacity for Na+ and K+ transport, has not been clearly delineated. We examined whether energy stress and/or AMPK affect expression of NKA subunits in rat L6 and primary human myotubes. Energy stress, induced by glucose deprivation, increased protein content of NKAα1 and NKAα2 in L6 myotubes, while decreasing the content of NKAα1 in human myotubes. Pharmacological AMPK activators (AICAR, A-769662, and diflunisal) modulated expression of NKA subunits, but their effects only partially mimicked those that occurred in response to glucose deprivation, indicating that AMPK does not mediate all effects of energy stress on NKA expression. Gene silencing of AMPKα1/α2 increased protein levels of NKAα1 in L6 myotubes and NKAα1 mRNA levels in human myotubes, while decreasing NKAα2 protein levels in L6 myotubes. Collectively, our results suggest a role for energy stress and AMPK in modulation of NKA expression in skeletal muscle. However, their modulatory effects were not conserved between L6 myotubes and primary human myotubes, which suggests that coupling between energy stress, AMPK, and regulation of NKA expression in vitro depends on skeletal muscle cell model.
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Affiliation(s)
- Anja Vidović
- Faculty of Medicine, Institute of Pathophysiology, University of Ljubljana, Ljubljana, Slovenia
| | - Klemen Dolinar
- Faculty of Medicine, Institute of Pathophysiology, University of Ljubljana, Ljubljana, Slovenia
| | - Alexander V Chibalin
- Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
- National Research Tomsk State University, Tomsk, Russia
| | - Sergej Pirkmajer
- Faculty of Medicine, Institute of Pathophysiology, University of Ljubljana, Ljubljana, Slovenia.
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2
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Kociper B, Škorja Milić N, Ogrizek I, Miš K, Pirkmajer S. Inhibition of the ubiquitin-proteasome system reduces the abundance of pyruvate dehydrogenase kinase 1 in cultured myotubes. J Muscle Res Cell Motil 2024; 45:155-169. [PMID: 39080182 DOI: 10.1007/s10974-024-09679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/05/2024] [Indexed: 08/11/2024]
Abstract
Pyruvate dehydrogenase kinase (PDK), which phosphorylates the pyruvate dehydrogenase complex, regulates glucose metabolism in skeletal muscle. PDK1, an isozyme whose expression is controlled by hypoxia-inducible factor-1α (HIF-1α), is thought to play a role in muscle adaptation to hypoxia. While transcriptional upregulation of PDK1 by HIF-1α is well characterised, mechanisms controlling proteolysis of PDK1 in skeletal muscle have not been thoroughly investigated. Proteasome inhibitor MG132 paradoxically reduced the abundance of PDK1 in human cancer cells and rat L6 myotubes, suggesting that MG132 might direct PDK1 towards autophagic degradation. The objectives of our current study were to determine (1) whether MG132 suppresses PDK1 levels in primary human myotubes, (2) whether chloroquine, an inhibitor of autophagy, prevents MG132-induced suppression of PDK1 in L6 myotubes, and (3) whether PYR-41, an inhibitor of ubiquitination, suppresses PDK1 in L6 myotubes. Using qPCR and/or immunoblotting, we found that despite markedly upregulating HIF-1α protein, MG132 did not alter the PDK1 expression in cultured primary human myotubes, while it suppressed both PDK1 mRNA and protein in L6 myotubes. The PDK1 levels in L6 myotubes were suppressed also during co-treatment with chloroquine and MG132. PYR-41 markedly increased the abundance of HIF-1α in primary human and L6 myotubes, while reducing the abundance of PDK1. In L6 myotubes treated with PYR-41, chloroquine increased the abundance of the epidermal growth factor receptor, but did not prevent the suppression of PDK1. Collectively, our results suggest that cultured myotubes degrade PDK1 via a pathway that cannot be inhibited by MG132, PYR-41, and/or chloroquine.
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Affiliation(s)
- Blaž Kociper
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia
| | - Nives Škorja Milić
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia
| | - Ivana Ogrizek
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia
| | - Katarina Miš
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia
| | - Sergej Pirkmajer
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia.
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3
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Koelink PJ, Gómez-Mellado VE, Duijst S, van Roest M, Meisner S, Ho-Mok KS, Frank S, Appelman BS, Bloemendaal LT, Vogel GF, van de Graaf SFJ, Bosma PJ, Oude Elferink RPJ, Wildenberg ME, Paulusma CC. The Phospholipid Flippase ATP8B1 is Involved in the Pathogenesis of Ulcerative Colitis via Establishment of Intestinal Barrier Function. J Crohns Colitis 2024; 18:1134-1146. [PMID: 38366839 PMCID: PMC11302967 DOI: 10.1093/ecco-jcc/jjae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024]
Abstract
AIMS Patients with mutations in ATP8B1 develop progressive familial intrahepatic cholestasis type 1 [PFIC1], a severe liver disease that requires life-saving liver transplantation. PFIC1 patients also present with gastrointestinal problems, including intestinal inflammation and diarrhoea, which are aggravated after liver transplantation. Here we investigate the intestinal function of ATP8B1 in relation to inflammatory bowel diseases. METHODS ATP8B1 expression was investigated in intestinal samples of patients with Crohn's disease [CD] or ulcerative colitis [UC] as well as in murine models of intestinal inflammation. Colitis was induced in ATP8B1-deficient mice with dextran sodium sulphate [DSS] and intestinal permeability was investigated. Epithelial barrier function was assessed in ATP8B1 knockdown Caco2-BBE cells. Co-immunoprecipitation experiments were performed in Caco2-BBE cells overexpressing ATP8B1-eGFP. Expression and localization of ATP8B1 and tight junction proteins were investigated in cells and in biopsies of UC and PFIC1 patients. RESULTS ATP8B1 expression was decreased in UC and DSS-treated mice, and was associated with a decreased tight junctional pathway transcriptional programme. ATP8B1-deficient mice were extremely sensitive to DSS-induced colitis, as evidenced by increased intestinal barrier leakage. ATP8B1 knockdown cells showed delayed barrier establishment that affected Claudin-4 [CLDN4] levels and localization. CLDN4 immunohistochemistry showed a tight junctional staining in control tissue, whereas in UC and intestinal PFIC1 samples, CLDN4 was not properly localized. CONCLUSION ATP8B1 is important in the establishment of the intestinal barrier. Downregulation of ATP8B1 levels in UC, and subsequent altered localization of tight junctional proteins, including CLDN4, might therefore be an important mechanism in UC pathophysiology.
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Affiliation(s)
- Pim J Koelink
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Valentina E Gómez-Mellado
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Suzanne Duijst
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Manon van Roest
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Sander Meisner
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Kam S Ho-Mok
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Sabrina Frank
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
| | - Babette S Appelman
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
| | - Lysbeth ten Bloemendaal
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Georg F Vogel
- Department of Paediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stan F J van de Graaf
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Piter J Bosma
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ronald P J Oude Elferink
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Manon E Wildenberg
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Coen C Paulusma
- Amsterdam University Medical Centers, University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
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4
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Dong C, Li F, Sun Y, Long D, Chen C, Li M, Wei T, Martins RP, Chen T, Mak PI. A syndromic diagnostic assay on a macrochannel-to-digital microfluidic platform for automatic identification of multiple respiratory pathogens. LAB ON A CHIP 2024; 24:3850-3862. [PMID: 37961846 DOI: 10.1039/d3lc00728f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The worldwide COVID-19 pandemic has changed people's lives and the diagnostic landscape. The nucleic acid amplification test (NAT) as the gold standard for SARS-CoV-2 detection has been applied in containing its transmission. However, there remains a lack of an affordable on-site detection system at resource-limited areas. In this study, a low cost "sample-in-answer-out" system incorporating nucleic acid extraction, purification, and amplification was developed on a single macrochannel-to-digital microfluidic chip. The macrochannel fluidic subsystem worked as a world-to-chip interface receiving 500-1000 μL raw samples, which then underwent bead-based extraction and purification processes before being delivered to DMF. Electrodes actuate an eluent dispensed to eight independent droplets for reverse transcription quantitative polymerase chain reaction (RT-qPCR). By reading with 4 florescence channels, the system can accommodate a maximum of 32 detection targets. To evaluate the proposed platform, a comprehensive assessment was conducted on the microfluidic chip as well as its functional components (i.e., extraction and amplification). The platform demonstrated a superior performance. In particular, using clinical specimens, the chip targeting SARS-CoV-2 and Flu A/B exhibited 100% agreement with off-chip diagnoses. Furthermore, the fabrication of chips is ready for scaled-up manufacturing and they are cost-effective for disposable use since they are assembled using a printed circuit board (PCB) and prefabricated blocks. Overall, the macrochannel-to-digital microfluidic platform coincides with the requirements of point-of-care testing (POCT) because of its advantages: low-cost, ease of use, comparable sensitivity and specificity, and availability for mass production.
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Affiliation(s)
- Cheng Dong
- School of Intelligent Systems Science and Engineering/JNU-Industry School of Artificial Intelligence, Jinan University, Zhuhai 519000, China
| | - Fei Li
- Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Yun Sun
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Dongling Long
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Chunzhao Chen
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhu Hai 519087, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, USA
| | - Tao Wei
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, 510640, China
- Pan Asia (Jiangmen) Institute of Biological Engineering and Health, Jiangmen, 529080, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
| | | | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
- Faculty of Science and Technology, University of Macau, Taipa, Macau SAR, 999078, China
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5
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Rose SA, Robicheau BM, Tolman J, Fonseca-Batista D, Rowland E, Desai D, Ratten JM, Kantor EJH, Comeau AM, Langille MG, Jerlström-Hultqvist J, Devred E, Sarthou G, Bertrand EM, LaRoche J. Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni. SCIENCE ADVANCES 2024; 10:eadn1476. [PMID: 39083619 PMCID: PMC11290528 DOI: 10.1126/sciadv.adn1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.
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Affiliation(s)
- Sonja A. Rose
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Debany Fonseca-Batista
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jenni-Marie Ratten
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ella Joy H. Kantor
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - André M. Comeau
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G.I. Langille
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Emmanuel Devred
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Halifax, Nova Scotia, Canada
| | | | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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6
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Dasgupta S, Sharapova T, Mahalingaiah PK, Chorley BN, Shoieb A, Tsuji T, Dos Santos AAC, Chari R, Ebrahimi A, Dalmas Wilk DA, Pettit S, Bawa B, Vaughan E, van Vleet TR, Mitchell CA, Yuen PST. Urinary MicroRNA biomarkers of nephrotoxicity in Macaca fascicularis. Regul Toxicol Pharmacol 2024; 151:105668. [PMID: 38936797 DOI: 10.1016/j.yrtph.2024.105668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/10/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Drug-induced kidney injury (DIKI) refers to kidney damage resulting from the administration of medications. The aim of this project was to identify reliable urinary microRNA (miRNAs) biomarkers that can be used as potential predictors of DIKI before disease diagnosis. This study quantified a panel of six miRNAs (miRs-210-3p, 423-5p, 143-3p, 130b-3p, 486-5p, 193a-3p) across multiple time points using urinary samples from a previous investigation evaluating effects of a nephrotoxicant in cynomolgus monkeys. Exosome-associated miRNA exhibited distinctive trends when compared to miRNAs quantified in whole urine, which may reflect a different urinary excretion mechanism of miRNAs than those released passively into the urine. Although further research and mechanistic studies are required to elucidate how these miRNAs regulate signaling in disease pathways, we present, for the first time, data that several miRNAs displayed strong correlations with histopathology scores, thus indicating their potential use as biomarkers to predict the development of DIKI in preclinical studies and clinical trials. Also, these findings can potentially be translated into other non-clinical species or human for the detection of DIKI.
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Affiliation(s)
- Subham Dasgupta
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | | | | | - Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Takayuki Tsuji
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alef A C Dos Santos
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rohit Chari
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Syril Pettit
- Health and Environmental Sciences Institute, Washington, DC, USA
| | | | | | | | | | - Peter S T Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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7
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Gasperoni JG, Tran SC, Grommen SVH, De Groef B, Dworkin S. The Role of PLAG1 in Mouse Brain Development and Neurogenesis. Mol Neurobiol 2024; 61:5851-5867. [PMID: 38240991 PMCID: PMC11249490 DOI: 10.1007/s12035-024-03943-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/10/2024] [Indexed: 07/16/2024]
Abstract
The pleomorphic adenoma gene 1 (Plag1) is a transcription factor involved in the regulation of growth and cellular proliferation. Here, we report the spatial distribution and functional implications of PLAG1 expression in the adult mouse brain. We identified Plag1 promoter-dependent β-galactosidase expression in various brain structures, including the hippocampus, cortex, choroid plexus, subcommisural organ, ependymal cells lining the third ventricle, medial and lateral habenulae and amygdala. We noted striking spatial-restriction of PLAG1 within the cornu ammonis (CA1) region of the hippocampus and layer-specific cortical expression, with abundant expression noted in all layers except layer 5. Furthermore, our study delved into the role of PLAG1 in neurodevelopment, focusing on its impact on neural stem/progenitor cell proliferation. Loss of Plag1 resulted in reduced proliferation and decreased production of neocortical progenitors in vivo, although ex vivo neurosphere experiments revealed no cell-intrinsic defects in the proliferative or neurogenic capacity of Plag1-deficient neural progenitors. Lastly, we explored potential target genes of PLAG1 in the cortex, identifying that Neurogenin 2 (Ngn2) was significantly downregulated in Plag1-deficient mice. In summary, our study provides novel insights into the spatial distribution of PLAG1 expression in the adult mouse brain and its potential role in neurodevelopment. These findings expand our understanding of the functional significance of PLAG1 within the brain, with potential implications for neurodevelopmental disorders and therapeutic interventions.
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Affiliation(s)
- Jemma G Gasperoni
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Stephanie C Tran
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Sylvia V H Grommen
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Biology, KU Leuven, B3000, Leuven, Belgium
| | - Bert De Groef
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Biology, KU Leuven, B3000, Leuven, Belgium
| | - Sebastian Dworkin
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3086, Australia.
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8
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Li Z, Chen Y, Han Y, Diao Z, Huang T, Feng L, Ma Y, Liu C, Tian M, Li J, Feng W, Zhao Z, Jiang J, Li J, Zhang R. Diagnostic performance of mpox virus (MPXV) real-time PCR assays: multicenter assessment and extended sensitivity analysis. Eur J Clin Microbiol Infect Dis 2024; 43:1597-1607. [PMID: 38833104 DOI: 10.1007/s10096-024-04865-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/27/2024] [Indexed: 06/06/2024]
Abstract
PURPOSE To comprehensively investigate the diagnostic performance of routinely used assays in MPXV testing, the National Center of Clinical Laboratories in China conducted a nationwide external quality assessment (EQA) scheme and an evaluated nine assays used by ≥ 5 laboratories in the EQA. METHODS MPXV virus-like particles with 2700, 900 and 300 copies/mL were distributed to 195 EQA laboratories. For extended analysis, triple-diluted samples from 9000 to 4.12 copies/mL were repeated 20 times using the assays employed by ≥ 5 laboratories. The diagnostic performance was assessed by analyzing EQA data and calculating the limits of detection (LODs). RESULTS The performance was competent in 87.69% (171/195) of the participants and 87.94% (175/199) of the datasets. The positive percentage agreements (PPAs) were greater than 99% for samples at 2700 and 900 copies/mL, and 95.60% (761/796) for samples at 300 copies/mL. The calculated LODs for the two clades ranged from 228.44 to 924.31 copies/mL and were greater than the LODs specified by the respective kits. EasyDiagnosis had the lowest calculated LODs and showed superior performance in EQA, whereas BioGerm and Sansure, with higher calculated LODs, did not perform well in EQA. CONCLUSION This study provides valuable information from the EQA data and evaluation of the diagnostic performance of MPXV detection assays. It also provided insights into reagent optimization and enabled prompt public health interventions for the outbreak.
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Affiliation(s)
- Ziqiang Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Tao Huang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Cong Liu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Meng Tian
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
- Peking University Fifth School of Clinical Medicine, Beijing, P. R. China
| | - Jing Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Wanyu Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Zihong Zhao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
- Peking University Fifth School of Clinical Medicine, Beijing, P. R. China
| | - Jian Jiang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
- National Center for Clinical Laboratories, Beijing Hospital, No. 1 Dahua Road, Dongdan, Beijing, 100730, P. R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology, Beijing, P. R. China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
- National Center for Clinical Laboratories, Beijing Hospital, No. 1 Dahua Road, Dongdan, Beijing, 100730, P. R. China.
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9
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Lescano López I, Torres JR, Cecchini NM, Alvarez ME. Arabidopsis DNA glycosylase MBD4L improves recovery of aged seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2021-2032. [PMID: 38963754 DOI: 10.1111/tpj.16907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024]
Abstract
DNA glycosylases initiate the base excision repair (BER) pathway by catalyzing the removal of damaged or mismatched bases from DNA. The Arabidopsis DNA glycosylase methyl-CpG-binding domain protein 4 like (MBD4L) is a nuclear enzyme triggering BER in response to the genotoxic agents 5-fluorouracil and 5-bromouracil. To date, the involvement of MBD4L in plant physiological processes has not been analyzed. To address this, we studied the enzyme functions in seeds. We found that imbibition induced the MBD4L gene expression by generating two alternative transcripts, MBD4L.3 and MBD4L.4. Gene activation was stronger in aged than in non-aged seeds. Seeds from mbd4l-1 mutants displayed germination failures when maintained under control or ageing conditions, while 35S:MBD4L.3/mbd4l-1 and 35S:MBD4L.4/mbd4l-1 seeds reversed these phenotypes. Seed nuclear DNA repair, assessed by comet assays, was exacerbated in an MBD4L-dependent manner at 24 h post-imbibition. Under this condition, the BER genes ARP, APE1L, and LIG1 showed higher expression in 35S:MBD4L.3/mbd4l-1 and 35S:MBD4L.4/mbd4l-1 than in mbd4l-1 seeds, suggesting that these components could coordinate with MBD4L to repair damaged DNA bases in seeds. Interestingly, the ATM, ATR, BRCA1, RAD51, and WEE1 genes associated with the DNA damage response (DDR) pathway were activated in mbd4l-1, but not in 35S:MBD4L.3/mbd4l-1 or 35S:MBD4L.4/mbd4l-1 seeds. These results indicate that MBD4L is a key enzyme of a BER cascade that operates during seed imbibition, whose deficiency would cause genomic damage detected by DDR, generating a delay or reduction in germination.
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Affiliation(s)
- Ignacio Lescano López
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, X5000HUA, Argentina
| | - José Roberto Torres
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, X5000HUA, Argentina
| | - Nicolás Miguel Cecchini
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, X5000HUA, Argentina
| | - María Elena Alvarez
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, X5000HUA, Argentina
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10
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Sinha AK, Laursen MF, Brinck JE, Rybtke ML, Hjørne AP, Procházková N, Pedersen M, Roager HM, Licht TR. Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota. Nat Microbiol 2024; 9:1964-1978. [PMID: 38918470 PMCID: PMC11306097 DOI: 10.1038/s41564-024-01737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
Tryptophan is catabolized by gut microorganisms resulting in a wide range of metabolites implicated in both beneficial and adverse host effects. How gut microbial tryptophan metabolism is directed towards indole, associated with chronic kidney disease, or towards protective indolelactic acid (ILA) and indolepropionic acid (IPA) is unclear. Here we used in vitro culturing and animal experiments to assess gut microbial competition for tryptophan and the resulting metabolites in a controlled three-species defined community and in complex undefined human faecal communities. The generation of specific tryptophan-derived metabolites was not predominantly determined by the abundance of tryptophan-metabolizing bacteria, but rather by substrate-dependent regulation of specific metabolic pathways. Indole-producing Escherichia coli and ILA- and IPA-producing Clostridium sporogenes competed for tryptophan within the three-species community in vitro and in vivo. Importantly, fibre-degrading Bacteroides thetaiotaomicron affected this competition by cross-feeding monosaccharides to E. coli. This inhibited indole production through catabolite repression, thus making more tryptophan available to C. sporogenes, resulting in increased ILA and IPA production. The fibre-dependent reduction in indole was confirmed using human faecal cultures and faecal-microbiota-transplanted gnotobiotic mice. Our findings explain why consumption of fermentable fibres suppresses indole production but promotes the generation of other tryptophan metabolites associated with health benefits.
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Affiliation(s)
- Anurag K Sinha
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Martin F Laursen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julius E Brinck
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten L Rybtke
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Pii Hjørne
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicola Procházková
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Mikael Pedersen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Tine R Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
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11
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Wikström T, Kim SH, Leverin AL, Wennerholm UB, Jacobsson B, Valentin L, Bennett PR, Terzidou V, Hagberg H. Association between miRNAs in serum at 10-14 gestational weeks and spontaneous preterm delivery. Acta Obstet Gynecol Scand 2024. [PMID: 39034527 DOI: 10.1111/aogs.14926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/09/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024]
Abstract
INTRODUCTION Preterm delivery (PTD) is the leading cause of death in children under 5 years of age. Cervical shortening detected by ultrasound can be used to predict PTD, but prediction is not perfect, and complementary diagnostic markers are needed. Recently, specific plasma microribonucleic acid (miRNAs) detected in early second trimester were shown to be associated with spontaneous PTD in high-risk women with a singleton pregnancy. The aim of this study was to explore to what extent these miRNAs are associated with spontaneous PTD and cervical length in a general population. MATERIAL AND METHODS This study is a nested case-control study within the CERVIX study. The CERVIX study evaluated the ability of cervical length screening with transvaginal ultrasound to identify women at risk of PTD. In the present study, women who delivered spontaneously <34 weeks (n = 61) were compared with a control group of women who delivered at full term (39 + 0 to 40 + 6 gestational weeks, n = 205). Archived serum samples were analyzed with RT-qPCR for miRNA expression levels of let-7a-5p, miR-150-5p, miR-15b-5p, miR-185-5p, miR-191-5p, miR-19b-3p, miR-23a-3p, miR-374a-5p, and miR-93-5p. The mean relative expression was compared between the groups. Sub-analyses were performed for women delivering <32, <30, and <28 weeks versus the full-term group. RESULTS The analyzed miRNAs were not significantly differentially expressed in women delivering <34 weeks compared to those delivering at full term. MiR-191-5p and miR-93-5p were significantly overexpressed in women who delivered <32 weeks, and further increase in fold change was observed with decreasing gestational age at delivery. The level of miR-15b-5p was significantly higher in women delivering at <30 weeks compared to those delivering at full term. CONCLUSIONS Our study shows that overexpression of miR-93-5p, miR-15b-5p, and miR-191-5p in serum at early gestation is associated with spontaneous PTD in a general population. Further research is needed to evaluate the potential of these miRNAs as future biomarkers for spontaneous PTD, as well as their pathophysiological role in spontaneous PTD.
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Affiliation(s)
- Tove Wikström
- Department of Obstetrics and Gynecology, Centre of Perinatal Medicine and Health, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sung Hye Kim
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Anna-Lena Leverin
- Department of Obstetrics and Gynecology, Centre of Perinatal Medicine and Health, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulla-Britt Wennerholm
- Department of Obstetrics and Gynecology, Centre of Perinatal Medicine and Health, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Centre of Perinatal Medicine and Health, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lil Valentin
- Department of Obstetrics and Gynecology, Skåne University Hospital, Malmö, Sweden
- Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Phillip R Bennett
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Vasso Terzidou
- Parturition Research Group, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Academic Department of Obstetrics and Gynaecology, Chelsea and Westminster Hospital, London, UK
| | - Henrik Hagberg
- Department of Obstetrics and Gynecology, Centre of Perinatal Medicine and Health, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
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12
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Alberca CD, Georgieff EI, Berardino BG, Ferroni NM, Fesser EA, Cantarelli VI, Ponzio MF, Cánepa ET, Chertoff M. Perinatal protein malnutrition alters maternal behavior and leads to maladaptive stress response, neurodevelopmental delay and disruption on DNA methylation machinery in female mice offspring. Horm Behav 2024; 164:105603. [PMID: 39029339 DOI: 10.1016/j.yhbeh.2024.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024]
Abstract
Deficiencies in maternal nutrition have long-term consequences affecting brain development of the progeny and its behavior. In the present work, female mice were exposed to a normal-protein or a low-protein diet during gestation and lactation. We analyzed behavioral and molecular consequences of malnutrition in dams and how it affects female offspring at weaning. We have observed that a low-protein diet during pregnancy and lactation leads to anxiety-like behavior and anhedonia in dams. Protein malnutrition during the perinatal period delays physical and neurological development of female pups. Glucocorticoid levels increased in the plasma of malnourished female offspring but not in dams when compared to the control group. Interestingly, the expression of glucocorticoid receptor (GR) was reduced in hippocampus and amygdala on both malnourished dams and female pups. In addition, malnourished pups exhibited a significant increase in the expression of Dnmt3b, Gadd45b, and Fkbp5 and a reduction in Bdnf VI variant mRNA in hippocampus. In contrast, a reduction on Dnmt3b has been observed on the amygdala of weaned mice. No changes have been observed on global methylation levels (5-methylcytosine) in hippocampal genomic DNA neither in dams nor female offspring. In conclusion, deregulated behaviors observed in malnourished dams might be mediated by a low expression of GR in brain regions associated with emotive behaviors. Additionally, low-protein diet differentially deregulates the expression of genes involved in DNA methylation/demethylation machinery in female offspring but not in dams, providing an insight into regional- and age-specific mechanisms due to protein malnutrition.
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Affiliation(s)
- Carolina D Alberca
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Erika I Georgieff
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Bruno G Berardino
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nadina M Ferroni
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Estefanía A Fesser
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica I Cantarelli
- Instituto de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, e Instituto de Investigaciones en Ciencias de la Salud (INICSA; CONICET-UNC), Santa Rosa 1085, X5000ESU Córdoba, Argentina
| | - Marina F Ponzio
- Instituto de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, e Instituto de Investigaciones en Ciencias de la Salud (INICSA; CONICET-UNC), Santa Rosa 1085, X5000ESU Córdoba, Argentina
| | - Eduardo T Cánepa
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Chertoff
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.
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13
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Hubinský M, Hobza R, Starczak M, Gackowski D, Kubát Z, Janíček T, Horáková L, Rodriguez Lorenzo JL. Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3849-3861. [PMID: 38652039 PMCID: PMC11233409 DOI: 10.1093/jxb/erae178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.
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Affiliation(s)
- Marcel Hubinský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lucie Horáková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jose Luis Rodriguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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14
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Visser N, Silva AV, Tarvainen I, Damdimopoulos A, Davey E, Roos K, Björvang RD, Kallak TK, Lager S, Lavogina D, Laws M, Piltonen T, Salumets A, Flaws JA, Öberg M, Velthut-Meikas A, Damdimopoulou P, Olovsson M. Epidemiologically relevant phthalates affect human endometrial cells in vitro through cell specific gene expression changes related to the cytoskeleton and mitochondria. Reprod Toxicol 2024; 128:108660. [PMID: 38992643 DOI: 10.1016/j.reprotox.2024.108660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/27/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Phthalates are endocrine disrupting chemicals (EDCs) found in common consumer products such as soft plastics and cosmetics. Although the knowledge regarding the adverse effects of phthalates on female fertility are accumulating, information on the hormone sensitive endometrium is still scarce. Here, we studied the effects of phthalates on endometrial cell proliferation and gene expression. Human endometrial primary epithelial and stromal cells were isolated from healthy fertile-aged women (n=3), and were compared to endometrial cell lines T-HESC and Ishikawa. Three different epidemiologically relevant phthalate mixtures were used, defined by urine samples in the Midlife Women Health Study (MWHS) cohort. Mono (2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) was used as a single phthalate control. Cells were harvested for proliferation testing and transcriptomic analyses after 24 h exposure. Even though all cell models responded differently to the phthalate exposures, many overlapping differentially expressed genes (DEGs, FDR<0.1), related to cell adhesion, cytoskeleton and mitochondria were found in all cell types. The qPCR analysis confirmed that MEHHP significantly affected cell adhesion gene vinculin (VCL) and NADH:ubiquinone oxidoreductase subunit B7 (NDUFB7), important for oxidative phosphorylation. Benchmark dose modelling showed that MEHHP had significant concentration-dependent effects on cytoskeleton gene actin-beta (ACTB). In conclusion, short 24 h phthalate exposures significantly altered gene expression cell-specifically in human endometrial cells, with six shared DEGs. The mixture effects were similar to those of MEHHP, suggesting MEHHP could be the main driver in the mixture. Impact of phthalate exposures on endometrial functions including receptivity should be addressed.
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Affiliation(s)
- Nadja Visser
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Antero Vieira Silva
- Unit of Integrative Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ilari Tarvainen
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm 17177, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Stockholm 17177, Sweden; Department of Obstetrics and Gynaecology, University of Helsinki, Helsinki University Central Hospital, Haartmaninkatu 8, Helsinki 00029 HUS, Finland
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Analysis Core Facility, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Eva Davey
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Kristine Roos
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Nova Vita Clinic, Tallinn, Estonia
| | - Richelle D Björvang
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden; Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm 17177, Sweden
| | | | - Susanne Lager
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Darja Lavogina
- Competence Centre on Health Technologies, Tartu, Estonia; Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Mary Laws
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Terhi Piltonen
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Centre, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Andres Salumets
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm 17177, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Stockholm 17177, Sweden; Competence Centre on Health Technologies, Tartu, Estonia; Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Jodi A Flaws
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Mattias Öberg
- Unit of Integrative Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Pauliina Damdimopoulou
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm 17177, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Stockholm 17177, Sweden
| | - Matts Olovsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.
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15
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Pereira AR, Redzic N, Van Vooren S, Pelak K, Broekmans A, Desloovere G, Vanden Broeck D, Kehoe K, Bogers J, Coppens A, Vreysen S, Mailleux J, Uten W. Development, Validation, and Implementation of an Augmented Multiwell, Multitarget Quantitative PCR for the Analysis of Human Papillomavirus Genotyping through Software Automation, Data Science, and Artificial Intelligence. J Mol Diagn 2024:S1525-1578(24)00149-1. [PMID: 38972594 DOI: 10.1016/j.jmoldx.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 05/02/2024] [Accepted: 05/20/2024] [Indexed: 07/09/2024] Open
Abstract
The value of human papillomavirus (HPV) testing for cervical cancer screening is well established; however, its use as a primary screening option or as a reflex test after atypical cytology results is now gaining wider acceptance. The importance of full genotyping and viral load determination has been demonstrated to enhance the clinical understanding of the viral infection progression during follow-up or after treatment, thereby providing clinicians with supplementary tools for optimized patient management. We developed a new analysis method for the RIATOL quantitative PCR assay, and validated and implemented it in the laboratory of clinical molecular pathology at Algemeen Medisch Laboratorium (AML), under national accreditation and following the International Organization for Standardization guidelines. This study presents the successful validation of a high-throughput, multitarget HPV analysis method, with enhanced accuracy on both qualitative and quantitative end results. This is achieved by software standardization and automation of PCR curve analysis and interpretation, using data science and artificial intelligence. Moreover, the user-centric functionality of the platform was demonstrated to enhance both staff training and routine analysis workflows, thereby saving time and laboratory personnel resources. Overall, the integration of the FastFinder plugin semi-automatic analysis algorithm with the RIATOL real-time quantitative PCR assay proved to be a remarkable advancement in high-throughput HPV quantification, with demonstrated capability to provide highly accurate clinical-grade results and to reduce manual variability and analysis time.
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Affiliation(s)
- A Rita Pereira
- Laboratory of Molecular Diagnostics, Algemeen Medisch Laboratorium (AML), Sonic Healthcare BeNeLux, Antwerp, Belgium.
| | - Nina Redzic
- Laboratory of Molecular Diagnostics, Algemeen Medisch Laboratorium (AML), Sonic Healthcare BeNeLux, Antwerp, Belgium; Applied Molecular Biology Research Group (AMBIOR), Laboratory for Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | - Davy Vanden Broeck
- Laboratory of Molecular Diagnostics, Algemeen Medisch Laboratorium (AML), Sonic Healthcare BeNeLux, Antwerp, Belgium; Applied Molecular Biology Research Group (AMBIOR), Laboratory for Cell Biology and Histology, University of Antwerp, Antwerp, Belgium; National Reference Centre for HPV, Brussels, Belgium; International Centre for Reproductive Health, Ghent University, Ghent, Belgium
| | - Kaat Kehoe
- Laboratory of Molecular Diagnostics, Algemeen Medisch Laboratorium (AML), Sonic Healthcare BeNeLux, Antwerp, Belgium; National Reference Centre for HPV, Brussels, Belgium
| | - Johannes Bogers
- Laboratory of Molecular Diagnostics, Algemeen Medisch Laboratorium (AML), Sonic Healthcare BeNeLux, Antwerp, Belgium; Applied Molecular Biology Research Group (AMBIOR), Laboratory for Cell Biology and Histology, University of Antwerp, Antwerp, Belgium; National Reference Centre for HPV, Brussels, Belgium
| | - Astrid Coppens
- Laboratory of Molecular Diagnostics, Algemeen Medisch Laboratorium (AML), Sonic Healthcare BeNeLux, Antwerp, Belgium
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16
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Rueda-Alaña E, Grillo M, Vázquez E, Salas SM, Senovilla-Ganzo R, Escobar L, Quintas A, Benguría A, Aransay AM, Bengoa-Vergniory N, Dopazo A, Encinas JM, Nilsson M, García-Moreno F. BirthSeq, a new method to isolate and analyze dated cells in different vertebrates. Development 2024; 151:dev202429. [PMID: 38856078 DOI: 10.1242/dev.202429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well documented, with evidence showing that time plays a crucial role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via fluorescence-activated cell sorting, and analysis using high-throughput techniques. We calibrated the BirthSeq method for developmental organs across three vertebrate species (mouse, chick and gecko), and utilized it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organisms, aiding developmental biology research by targeting cells and their temporal cues.
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Affiliation(s)
- Eneritz Rueda-Alaña
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Marco Grillo
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Enrique Vázquez
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Sergio Marco Salas
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Rodrigo Senovilla-Ganzo
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Laura Escobar
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Ana Quintas
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Alberto Benguría
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Ana María Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Nora Bengoa-Vergniory
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Juan Manuel Encinas
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
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17
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Volpe C, Nymark M, Andersen T, Winge P, Lavaud J, Vadstein O. Skeletonema marinoi ecotypes show specific habitat-related responses to fluctuating light supporting high potential for growth under photobioreactor light regime. THE NEW PHYTOLOGIST 2024; 243:145-161. [PMID: 38736026 DOI: 10.1111/nph.19788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
Diatoms are a diverse group of phytoplankton usually dominating areas characterized by rapidly shifting light conditions. Because of their high growth rates and interesting biochemical profile, their biomass is considered for various commercial applications. This study aimed at identifying strains with superior growth in a photobioreactor (PBR) by screening the natural intraspecific diversity of ecotypes isolated from different habitats. We investigated the effect of PBR light fluctuating on a millisecond scale (FL, simulating the light in a PBR) on 19 ecotypes of the diatom Skeletonema marinoi isolated from the North Sea-Baltic Sea area. We compare growth, pigment ratios, phylogeny, photo-physiological variables and photoacclimation strategies between all strains and perform qPCR and absorption spectra analysis on a subset of strains. Our results show that the ecotypes responded differently to FL, and have contrasting photo-physiological and photoprotective strategies. The strains from Kattegat performed better in FL, and shared common photoacclimation and photoprotection strategies that are the results of adaptation to the specific light climate of the Kattegat area. The strains that performed better with FL conditions had a high light (HL)-acclimated phenotype coupled with unique nonphotochemical quenching features. Based on their characteristics, three strains were identified as good candidates for growth in PBRs.
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Affiliation(s)
- Charlotte Volpe
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, N-7465, Trondheim, Norway
| | - Marianne Nymark
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, N-7465, Trondheim, Norway
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Tom Andersen
- Department of Biosciences, Section for Aquatic Biology and Toxicology (AQUA), University of Oslo, N-0316, Oslo, Norway
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Johann Lavaud
- LEMAR-Laboratory of Marine Environmental Sciences, UMR6539 CNRS, Univ Brest, Ifremer, IRD, Institut Européen de la Mer, Technopôle Brest-Iroise, rue Dumont d'Urville, Plouzané, 29280, France
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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18
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Colman SL, Salcedo MF, Iglesias MJ, Alvarez VA, Fiol DF, Casalongué CA, Foresi NP. Chitosan microparticles mitigate nitrogen deficiency in tomato plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108728. [PMID: 38772165 DOI: 10.1016/j.plaphy.2024.108728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/23/2024]
Abstract
Nitrogen (N) deficiency is one of the most prevalent nutrient deficiencies in plants, and has a significant impact on crop yields. In this work we aimed to develop and evaluate innovative strategies to mitigate N deficiency. We studied the effect of supplementing tomato plants grown under suboptimal N nutrition with chitosan microparticles (CS-MPs) during short- and long-term periods. We observed that the supplementation with CS-MPs prevented the reduction of aerial biomass and the elongation of lateral roots (LR) triggered by N deficiency in tomato plantlets. In addition, levels of nitrates, amino acids and chlorophyll, which decreased drastically upon N deficiency, were either partial or totally restored upon CS-MPs addition to N deficient media. Finally, we showed that CS-MPs treatments increased nitric oxide (NO) levels in root tips and caused the up-regulation of genes involved in N metabolism. Altogether, we suggest that CS-MPs enhance the growth and development of tomato plants under N deficiency through the induction of biochemical and transcriptional responses that lead to increased N metabolism. We propose treatments with CS-MPs as an efficient practice focused to mitigate the nutritional deficiencies in N impoverished soils.
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Affiliation(s)
- Silvana Lorena Colman
- Instituto de Investigaciones Biológicas (IIB), UE CONICET-UNMdP, FCEyN, Mar Del Plata, Argentina.
| | - María Florencia Salcedo
- Instituto de Investigaciones Biológicas (IIB), UE CONICET-UNMdP, FCEyN, Mar Del Plata, Argentina
| | - María José Iglesias
- Instituto de Investigaciones Biológicas (IIB), UE CONICET-UNMdP, FCEyN, Mar Del Plata, Argentina
| | - Vera Alejandra Alvarez
- Instituto de Investigación en Ciencia & Tecnología de Materiales (INTEMA), UE CONICET-UNMdP, Grupo Materiales Compuestos Termoplásticos (CoMP), Mar Del Plata, Argentina
| | - Diego Fernando Fiol
- Instituto de Investigaciones Biológicas (IIB), UE CONICET-UNMdP, FCEyN, Mar Del Plata, Argentina
| | | | - Noelia Pamela Foresi
- Instituto de Investigaciones Biológicas (IIB), UE CONICET-UNMdP, FCEyN, Mar Del Plata, Argentina.
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19
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Amalraj A, Baumann U, Hayes JE, Sutton T. Using RNA sequencing to unravel molecular changes underlying the defense response in chickpea induced by Phytophthora medicaginis. PHYSIOLOGIA PLANTARUM 2024; 176:e14412. [PMID: 38952339 DOI: 10.1111/ppl.14412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/03/2024]
Abstract
Phytophthora root rot (PRR), caused by Phytophthora medicaginis, is a major soil-borne disease of chickpea in Australia. Breeding for PRR resistance is an effective approach to avoid significant yield loss. Genetic resistance has been identified in cultivated chickpea (Cicer arietinum) and in the wild relative C. echinospermum, with previous studies identifying independent genetic loci associated with each of these sources. However, the molecular mechanisms associated with PRR resistance are not known. RNA sequencing analysis employed in this study identified changes in gene expression in roots of three chickpea genotypes grown hydroponically, early post-infection with P. medicaginis zoospores. Analyses of differentially expressed genes (DEG) identified the activation of a higher number of non-specific R-genes in a PRR-susceptible variety than in the resistant genotypes, suggesting a whole plant resistance response occurring in chickpea against the pathogen. Contrasting molecular changes in signaling profiles, proteolysis and transcription factor pathways were observed in the cultivated and wild Cicer-derived resistant genotypes. DEG patterns supported a hypothesis that increased root elongation and reduced adventitious root formation limit the pathogen entry points in the genotype containing the wild Cicer source of PRR resistance. Candidate resistance genes, including an aquaporin and a maltose transporter in the wild Cicer source and GDSL esterases/lipases in the cultivated source of resistance, were oppositely regulated. Increased knowledge of these genes and pathways will improve our understanding of molecular mechanisms controlling PRR resistance in chickpea, and support the development of elite chickpea varieties through molecular breeding approaches.
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Affiliation(s)
- Amritha Amalraj
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, SA, Australia
| | - Ute Baumann
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, SA, Australia
| | - Julie E Hayes
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, SA, Australia
| | - Tim Sutton
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, SA, Australia
- South Australian Research and Development Institute (SARDI), SA, Australia
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20
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Omran TA, Tunsjø HS, Jahanlu D, Brackmann SA, Bemanian V, Sæther PC. Decoding immune-related gene-signatures in colorectal neoplasia. Front Immunol 2024; 15:1407995. [PMID: 38979413 PMCID: PMC11229009 DOI: 10.3389/fimmu.2024.1407995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Background Colorectal cancer (CRC) is a significant health issue, with notable incidence rates in Norway. The immune response plays a dual role in CRC, offering both protective effects and promoting tumor growth. This research aims to provide a detailed screening of immune-related genes and identify specific genes in CRC and adenomatous polyps within the Norwegian population, potentially serving as detection biomarkers. Methods The study involved 69 patients (228 biopsies) undergoing colonoscopy, divided into CRC, adenomatous polyps, and control groups. We examined the expression of 579 immune genes through nCounter analysis emphasizing differential expression in tumor versus adjacent non-tumorous tissue and performed quantitative reverse transcription polymerase chain reaction (RT-qPCR) across patient categories. Results Key findings include the elevated expression of CXCL1, CXCL2, IL1B, IL6, CXCL8 (IL8), PTGS2, and SPP1 in CRC tissues. Additionally, CXCL1, CXCL2, IL6, CXCL8, and PTGS2 showed significant expression changes in adenomatous polyps, suggesting their early involvement in carcinogenesis. Conclusions This study uncovers a distinctive immunological signature in colorectal neoplasia among Norwegians, highlighting CXCL1, CXCL2, IL1B, IL6, CXCL8, PTGS2, and SPP1 as potential CRC biomarkers. These findings warrant further research to confirm their role and explore their utility in non-invasive screening strategies.
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Affiliation(s)
- Thura Akrem Omran
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Hege Smith Tunsjø
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - David Jahanlu
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Stephan Andreas Brackmann
- Division of Medicine, Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vahid Bemanian
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Per Christian Sæther
- Department of Immunology and Transfusion Medicine, Akershus University Hospital, Lørenskog, Norway
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21
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Bagheri A, Nazari H, Shams-Esfandabadi N, Ahmadi E, Afzali A, Davoodian N, Nazifi S, Shirian S. Vitamin C Synergistically Enhances Protective Effects of Vitamin E Against Preantral Follicle Degeneration of Ovine Vitrified/Warmed Ovarian Tissue. Biopreserv Biobank 2024. [PMID: 38905140 DOI: 10.1089/bio.2022.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024] Open
Abstract
This study aimed to evaluate whether the addition of vitamins E and C as two conventional antioxidants improves the cryotolerance of preantral follicles enclosed in ovine ovarian tissue slices. For this purpose, ovarian slices were obtained from abattoired juvenile lambs and randomly distributed to the following groups: fresh, toxicity, vitrified (control), and three treatment groups in two experiments. Vitamin E, vitamin C, or vitamin E + C was added to the vitrification media alone in the first experiment and added to all vitrification, warming, and culture media in the second experiment. Finally, the treated tissues were cultured in vitro for 12 hours. The histological analysis showed that single or combined use of vitamins E and C increases intact preantral follicles in comparison to the control in two experiments (p < 0.05), and simultaneous use of vitamins E and C had a synergistic effect on increasing the percentage of normal preantral follicles in experiment 2 (p < 0.05). Due to the better results in Experiment 2, stromal cell density, antioxidant activity, and molecular evaluation were followed only in this experiment. The vitamin E + C group had higher stromal cell density compared with control group (p < 0.05). Vitamin E strengthened antioxidant capacity compared with the control and vitamin C groups (p < 0.05). This effect was exacerbated when used in combination with vitamin C (p < 0.05). The expression of all evaluated genes (BMP4, BMP15, GDF9, and KITLG) was significantly increased in ovarian tissue treated with vitamin E + C compared with the control group (p < 0.05). This increase was also observed in BMP4, GDF9, and KITLG genes compared with the vitamin C group (p < 0.05). In conclusion, this study revealed the positive effects of vitamins E and C on preantral follicle viability and to some extent a synergistic action of vitamin C on the protective effects of vitamin E against preantral follicle degeneration and increasing antioxidant capacity and development of preantral follicles after ovine ovarian tissue vitrification.
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Affiliation(s)
- Azita Bagheri
- Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Hassan Nazari
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Naser Shams-Esfandabadi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Ebrahim Ahmadi
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Azita Afzali
- Faculty of Medical Sciences, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Najmeh Davoodian
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Sina Nazifi
- Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Sadegh Shirian
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
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22
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Martinez-Sanchez M, Hunter DA, Saei A, Andre CM, Varkonyi-Gasic E, Clark G, Barry E, Allan AC. SmuMYB113 is the determinant of fruit color in pepino ( Solanum muricatum). FRONTIERS IN PLANT SCIENCE 2024; 15:1408202. [PMID: 38966143 PMCID: PMC11222579 DOI: 10.3389/fpls.2024.1408202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/03/2024] [Indexed: 07/06/2024]
Abstract
Pepino (Solanum muricatum) is an herbaceous crop phylogenetically related to tomato and potato. Pepino fruit vary in color, size and shape, and are eaten fresh. In this study, we use pepino as a fruit model to understand the transcriptional regulatory mechanisms controlling fruit quality. To identify the key genes involved in anthocyanin biosynthesis in pepino, two genotypes were studied that contrasted in foliar and fruit pigmentation. Anthocyanin profiles were analyzed, as well as the expression of genes that encode enzymes for anthocyanin biosynthesis and transcriptional regulators using both RNA-seq and quantitative PCR. The differential expression of the transcription factor genes R2R3 MYB SmuMYB113 and R3MYB SmuATV suggested their association with purple skin and foliage phenotype. Functional analysis of these genes in both tobacco and pepino showed that SmuMYB113 activates anthocyanins, while SmuATV suppresses anthocyanin accumulation. However, despite elevated expression in all tissues, SmuMYB113 does not significantly elevate flesh pigmentation, suggesting a strong repressive background in fruit flesh tissue. These results will aid understanding of the differential regulation controlling fruit quality aspects between skin and flesh in other fruiting species.
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Affiliation(s)
- Marcela Martinez-Sanchez
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Donald A. Hunter
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Ali Saei
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Christelle M. Andre
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
| | - Glen Clark
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
| | - Emma Barry
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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23
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Vicentin L, Canales J, Calderini DF. The trade-off between grain weight and grain number in wheat is explained by the overlapping of the key phases determining these major yield components. FRONTIERS IN PLANT SCIENCE 2024; 15:1380429. [PMID: 38919825 PMCID: PMC11196766 DOI: 10.3389/fpls.2024.1380429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024]
Abstract
Enhancing grain yield is a primary goal in the cultivation of major staple crops, including wheat. Recent research has focused on identifying the physiological and molecular factors that influence grain weight, a critical determinant of crop yield. However, a bottleneck has arisen due to the trade-off between grain weight and grain number, whose underlying causes remain elusive. In a novel approach, a wheat expansin gene, TaExpA6, known for its expression in root tissues, was engineered to express in the grains of the spring wheat cultivar Fielder. This modification led to increases in both grain weight and yield without adversely affecting grain number. Conversely, a triple mutant line targeting the gene TaGW2, a known negative regulator of grain weight, resulted in increased grain weight but decreased grain number, potentially offsetting yield gains. This study aimed to evaluate the two aforementioned modified wheat genotypes (TaExpA6 and TaGW2) alongside their respective wild-type counterparts. Conducted in southern Chile, the study employed a Complete Randomized Block Design with four replications, under well-managed field conditions. The primary metrics assessed were grain yield, grain number, and average grain weight per spike, along with detailed measurements of grain weight and dimensions across the spike, ovary weight at pollination (Waddington's scale 10), and post-anthesis expression levels of TaExpA6 and TaGW2. Results indicated that both the TaExpA6 and the triple mutant lines achieved significantly higher average grain weights compared to their respective wild types. Notably, the TaExpA6 line did not exhibit a reduction in grain number, thereby enhancing grain yield per spike. By contrast, the triple mutant line showed a reduced grain number per spike, with no significant change in overall yield. TaExpA6 expression peaked at 10 days after anthesis (DAA), and its effect on grain weight over the WT became apparent after 15 DAA. In contrast, TaGW2 gene disruption in the triple mutant line increased ovary size at anthesis, leading to improved grain weight above the WT from the onset of grain filling. These findings suggest that the trade-off between grain weight and number could be attributed to the overlapping of the critical periods for the determination of these traits.
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Affiliation(s)
- Lucas Vicentin
- Graduate School, Faculty of Agricultural Science, Universidad Austral de Chile, Valdivia, Chile
- Institute of Plant Production and Protection, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Canales
- Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
- National Agency for Research and Development of Chile-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Daniel F. Calderini
- Institute of Plant Production and Protection, Universidad Austral de Chile, Valdivia, Chile
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24
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Vela-Alcántara AM, Santiago-García J, Barragán-Palacios M, León-Chacón A, Domínguez-Pantoja M, Barceinas-Dávila I, Juárez-Aguilar E, Tamariz E. Differential modulation of cell morphology, migration, and Neuropilin-1 expression in cancer and non-cancer cell lines by substrate stiffness. Front Cell Dev Biol 2024; 12:1352233. [PMID: 38903533 PMCID: PMC11188430 DOI: 10.3389/fcell.2024.1352233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/10/2024] [Indexed: 06/22/2024] Open
Abstract
Physical changes in the tumor microenvironment, such as increased stiffness, regulate cancer hallmarks and play an essential role in gene expression, cell morphology, migration, and malignancy. However, the response of cancer cells to stiffness is not homogeneous and varies depending on the cell type and its mechanosensitivity. In this study, we investigated the differential responses of cervical (HeLa) and prostate (PC-3) cancer cell lines, as well as non-tumoral cell lines (HEK293 and HPrEC), to stiffness using polyacrylamide hydrogels mimicking normal and tumoral tissues. We analyzed cell morphology, migration, and the expression of neuropilin 1 (NRP1), a receptor involved in angiogenesis, cell migration, and extracellular matrix remodeling, known to be associated with cancer progression and poor prognosis. Our findings reveal that NRP1 expression increases on substrates mimicking the high stiffness characteristic of tumoral tissue in the non-tumoral cell lines HPrEC and HEK293. Conversely, in tumoral PC-3 cells, stiffness resembling normal prostate tissue induces an earlier and more sustained expression of NRP1. Furthermore, we observed that stiffness influences cell spreading, pseudopodia formation, and the mode of cell protrusion during migration. Soft substrates predominantly trigger bleb cell protrusion, while pseudopodia protrusions increase on substrates mimicking normal and tumor-like stiffnesses in HPrEC cells compared to PC-3 cells. Stiffer substrates also enhance the percentage of migratory cells, as well as their velocity and total displacement, in both non-tumoral and tumoral prostate cells. However, they only improve the persistence of migration in tumoral PC-3 cells. Moreover, we found that NRP1 co-localizes with actin, and its suppression impairs tumoral PC-3 spreading while decreasing pseudopodia protrusion mode. Our results suggest that the modulation of NRP1 expression by the stiffness can be a feedback loop to promote malignancy in non-tumoral and cancer cells, contingent upon the mechanosensitivity of the cells.
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Affiliation(s)
- Ana Monserrat Vela-Alcántara
- Programa de Doctorado en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
- Laboratorio de Cultivo Celular, Departamento de Biomedicina, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
| | - Juan Santiago-García
- Laboratorio de Biología Molecular, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, Mexico
| | - Madeleine Barragán-Palacios
- Laboratorio de Cultivo Celular, Departamento de Biomedicina, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
| | - Aylin León-Chacón
- Laboratorio de Cultivo Celular, Departamento de Biomedicina, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
| | | | - Irene Barceinas-Dávila
- Laboratorio de Cultivo Celular, Departamento de Biomedicina, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
| | - Enrique Juárez-Aguilar
- Laboratorio de Cultivo Celular, Departamento de Biomedicina, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
| | - Elisa Tamariz
- Laboratorio de Cultivo Celular, Departamento de Biomedicina, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Mexico
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Frank CE, Sadeghi J, Heath DD, Semeniuk CAD. Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha). GENES, BRAIN, AND BEHAVIOR 2024; 23:e12898. [PMID: 38817102 PMCID: PMC11140169 DOI: 10.1111/gbb.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024]
Abstract
Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g., improved immune response, growth, and metabolism), we explored probiotic supplementation (mixture of Bifidobacterium, Lactobacillus, and Lactococcus), to overcome drawbacks. We first examined fish gut bacterial community composition using 16S metabarcoding (via principal coordinate analyses and PERMANOVA) and determined probiotics significantly impacted gut bacteria composition (p = 0.001). Secondly, we examined how a genomic disruptor (triploidy) and diet supplements (probiotics) impact gene transcription and behavioral profiles of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Juveniles from four treatment groups (diploid-regular feed, diploid-probiotic feed, triploid-regular feed, and triploid-probiotic feed; n = 360) underwent behavioral assays to test activity, exploration, neophobia, predator evasion, aggression/sociality, behavioral sensitivity, and flexibility. In these fish, transcriptional profiles for genes associated with neural functions (neurogenesis/synaptic plasticity) and biomarkers for stress response and development (growth/appetite) were (i) examined across treatments and (ii) used to describe behavioral phenotypes via principal component analyses and general linear mixed models. Triploids exhibited a more active behavioral profile (p = 0.002), and those on a regular diet had greater Neuropeptide Y transcription (p = 0.02). A growth gene (early growth response protein 1, p = 0.02) and long-term neural development genes (neurogenic differentiation factor, p = 0.003 and synaptysomal-associated protein 25-a, p = 0.005) impacted activity and reactionary profiles, respectively. Overall, our probiotic treatment did not compensate for triploidy. Our research highlights novel applications of behavioral transcriptomics for identifying candidate genes and dynamic, mechanistic associations with complex behavioral repertoires.
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Affiliation(s)
- Chelsea E. Frank
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
| | - Javad Sadeghi
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorOntarioCanada
| | - Daniel D. Heath
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorOntarioCanada
| | - Christina A. D. Semeniuk
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorOntarioCanada
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Dittmar MC, Tohidnezhad M, Fragoulis A, Bücker A, Stein M, Pufe T, Kubo Y. Pharmacological effects of methysticin and L-sulforaphane through the Nrf2/ARE signaling pathway in MLO-Y4 osteocytes: in vitro study. Ann Anat 2024; 254:152260. [PMID: 38521364 DOI: 10.1016/j.aanat.2024.152260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/04/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Oxidative stress plays a crucial role in the pathogenesis of many skeletal diseases by inducing osteocyte death. The transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) is a master regulator of various antioxidant gene expressions through antioxidant response element (ARE) against cellular oxidative stress and can be induced by various stimulants, including the phytochemicals methysticin (MET) and L-sulforaphane (SFN). This study aimed to establish an osteocyte in vitro model to investigate the pharmacological effects of MET and SFN on the Nrf2/ARE pathway. METHODS MLO-Y4 murine osteocytes and the stably transduced MLO-Y4-SIN-lenti-ARE reporter gene cell line were used. MET and SFN were used as Nrf2 inducers. The cytotoxicity of MET, SFN, and hydrogen peroxide (H2O2) was evaluated using the CytoTox-Glo™ Assay. Time- and dose-dependent ARE induction was examined by Monoluciferase Assay. The mRNA and protein expressions of Nrf2 target markers, such as heme-oxygenase 1 (Ho-1), NADPH quinone dehydrogenase 1 (Nqo1), and thioredoxin reductase 1 (Txnrd1), were detected by RT-qPCR, Western Blot, and immunofluorescence staining, respectively. Osteogenesis markers, osteopontin, and osteocalcin were compared with and without treatment by immunofluorescence staining. RESULTS The experimental data showed that MET and SFN induced ARE activity in a time- and dose-dependent manner and increased the mRNA and protein expression of antioxidant markers compared to vehicle-treated controls. The protein expression of osteopontin and osteocalcin in the samples treated with SFN were significantly higher than without treatment, and the number of cell death treated with SFN was significantly lower than without treatment under H2O2-induced stress conditions. CONCLUSIONS Nrf2 inducers MET and SFN increased the mRNA expression of antioxidant genes through the Nrf2/ARE pathway in osteocytes. Notably, SFN increased the protein expression of osteocyte-associated osteogenic markers and suppressed cell death under H2O2-induced stress condition. Thus, Nrf2 stimulators can exert stress-relieving and osteogenic effects on osteocytes.
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Affiliation(s)
- Maja Charlotte Dittmar
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany
| | - Mersedeh Tohidnezhad
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany
| | - Athanassios Fragoulis
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany
| | - Annette Bücker
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany
| | - Matthias Stein
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany
| | - Thomas Pufe
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany
| | - Yusuke Kubo
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Wendlingweg 2, Aachen 52074, Germany; Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Politiek FA, Turkenburg M, Henneman L, Ofman R, Waterham HR. Molecular and cellular consequences of mevalonate kinase deficiency. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167177. [PMID: 38636615 DOI: 10.1016/j.bbadis.2024.167177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/06/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Mevalonate kinase deficiency (MKD) is an autosomal recessive metabolic disorder associated with recurrent autoinflammatory episodes. The disorder is caused by bi-allelic loss-of-function variants in the MVK gene, which encodes mevalonate kinase (MK), an early enzyme in the isoprenoid biosynthesis pathway. To identify molecular and cellular consequences of MKD, we studied primary fibroblasts from severely affected patients with mevalonic aciduria (MKD-MA) and more mildly affected patients with hyper IgD and periodic fever syndrome (MKD-HIDS). As previous findings indicated that the deficient MK activity in MKD impacts protein prenylation in a temperature-sensitive manner, we compared the subcellular localization and activation of the small Rho GTPases RhoA, Rac1 and Cdc42 in control, MKD-HIDS and MKD-MA fibroblasts cultured at physiological and elevated temperatures. This revealed a temperature-induced altered subcellular localization and activation in the MKD cells. To study if and how the temperature-induced ectopic activation of these signalling proteins affects cellular processes, we performed comparative transcriptome analysis of control and MKD-MA fibroblasts cultured at 37 °C or 40 °C. This identified cell cycle and actin cytoskeleton organization as respectively most down- and upregulated gene clusters. Further studies confirmed that these processes were affected in fibroblasts from both patients with MKD-MA and MKD-HIDS. Finally, we found that, similar to immune cells, the MK deficiency causes metabolic reprogramming in MKD fibroblasts resulting in increased expression of genes involved in glycolysis and the PI3K/Akt/mTOR pathway. We postulate that the ectopic activation of small GTPases causes inappropriate signalling contributing to the molecular and cellular aberrations observed in MKD.
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Affiliation(s)
- Frouwkje A Politiek
- Laboratory Genetic Metabolic Diseases, Department of Laboratory Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Marjolein Turkenburg
- Laboratory Genetic Metabolic Diseases, Department of Laboratory Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Linda Henneman
- Laboratory Genetic Metabolic Diseases, Department of Laboratory Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands; Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rob Ofman
- Laboratory Genetic Metabolic Diseases, Department of Laboratory Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Laboratory Medicine, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands.
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28
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Ynsaurralde-Rivolta AE, Gambini A, Alberio V, Savy V, Ratner L, Guberman A, Vázquez Echegaray C, Gismondi MI, Currá A, Bevacqua R, Salamone D. In vitro developmental competence of bovine demi-embryos generated by blastomere separation and blastocyst bisection. Reprod Domest Anim 2024; 59:e14627. [PMID: 38837827 DOI: 10.1111/rda.14627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
The efficiency of bovine in vitro embryo production can be significantly improved by splitting embryos at different stages. However, the blastocyst quality of in vitro-produced demi-embryos remains unexplored. The objective of this research was to compare embryo developmental rates and quality of bovine demi-embryos produced by two different strategies: (a) embryo bisection (BSEC) and (b) 2-cell blastomere separation (BSEP). To determine demi-embryos quality, we evaluated total blastocyst cell number and proportion of SOX2+ cells. Additionally, the expression of SOX2, NANOG, OCT4, CDX2, IFNT, BAX and BCL genes and let-7a and miRNA-30c Micro RNAs was analysed. BSEP resulted in improved blastocyst development, higher ICM cells and a significantly higher expression of IFNΤ than demi-embryos produced by BSEC. Let-7a, which is associated with low pregnancy establishment was detected in BSEC, while miRNA-30c expression was observed in all treatments. In conclusion, BSEP of 2-cell embryos is more efficient to improve in vitro bovine embryo development and to produce good quality demi-embryos based on ICM cell number and the expression pattern of the genes explored compared to BSEC.
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Affiliation(s)
- A E Ynsaurralde-Rivolta
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - A Gambini
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - V Alberio
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - V Savy
- Reproductive and Developmental Biology Laboratory, Durham, North Carolina, USA
| | - L Ratner
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - A Guberman
- IQUIBICEN-CONICET Department of Biological Chemistry, FCEN, UBA, Buenos Aires, Argentina
| | - C Vázquez Echegaray
- IQUIBICEN-CONICET Department of Biological Chemistry, FCEN, UBA, Buenos Aires, Argentina
| | - M I Gismondi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - A Currá
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - R Bevacqua
- Mount Sinai, DOMI, New York, New York, USA
| | - D Salamone
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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Lang BJ, Holton KM, Guerrero-Gimenez ME, Okusha Y, Magahis PT, Shi A, Neguse M, Venkatesh S, Nhu AM, Gestwicki JE, Calderwood SK. Heat shock protein 72 supports extracellular matrix production in metastatic mammary tumors. Cell Stress Chaperones 2024; 29:456-471. [PMID: 38703814 PMCID: PMC11127224 DOI: 10.1016/j.cstres.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/28/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024] Open
Abstract
This study identified tumorigenic processes most dependent on murine heat shock protein 72 (HSP72) in the mouse mammary tumor virus-PyMT mammary tumor model, which give rise to spontaneous mammary tumors that exhibit HSP72-dependent metastasis to the lung. RNA-seq expression profiling of Hspa1a/Hspa1b (Hsp72) WT and Hsp72-/- primary mammary tumors discovered significantly lower expression of genes encoding components of the extracellular matrix (ECM) in Hsp72 knockout mammary tumors compared to WT controls. In vitro studies found that genetic or chemical inhibition of HSP72 activity in cultured collagen-expressing human or murine cells also reduces mRNA and protein levels of COL1A1 and several other ECM-encoding genes. In search of a possible mechanistic basis for this relationship, we found HSP72 to support the activation of the tumor growth factor-β-suppressor of mothers against decapentaplegic-3 signaling pathway and evidence of suppressor of mothers against decapentaplegic-3 and HSP72 coprecipitation, suggesting potential complex formation. Human COL1A1 mRNA expression was found to have prognostic value for HER2+ breast tumors over other breast cancer subtypes, suggesting a possible human disease context where targeting HSP72 may have a therapeutic rationale. Analysis of human HER2+ breast tumor gene expression data using a gene set comprising ECM-related gene and protein folding-related gene as an input to the statistical learning algorithm, Galgo, found a subset of these genes that can collectively stratify patients by relapse-free survival, further suggesting a potential interplay between the ECM and protein-folding genes may contribute to tumor progression.
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Affiliation(s)
- Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | | | - Martin E Guerrero-Gimenez
- Institute of Biochemistry and Biotechnology, School of Medicine, National University of Cuyo, Mendoza, Argentina
| | - Yuka Okusha
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Patrick T Magahis
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Amy Shi
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Mary Neguse
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shreya Venkatesh
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Anh M Nhu
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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Thirulogachandar V, Govind G, Hensel G, Kale SM, Kuhlmann M, Eschen-Lippold L, Rutten T, Koppolu R, Rajaraman J, Palakolanu SR, Seiler C, Sakuma S, Jayakodi M, Lee J, Kumlehn J, Komatsuda T, Schnurbusch T, Sreenivasulu N. HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2900-2916. [PMID: 38366171 DOI: 10.1093/jxb/erae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | | | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sudhakar Reddy Palakolanu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Christiane Seiler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
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Wieser NV, Ghiboub M, Verseijden C, van Goudoever JB, Schoonderwoerd A, de Meij TGJ, Niemarkt HJ, Davids M, Lefèvre A, Emond P, Derikx JPM, de Jonge WJ, Sovran B. Exploring the Immunomodulatory Potential of Human Milk: Aryl Hydrocarbon Receptor Activation and Its Impact on Neonatal Gut Health. Nutrients 2024; 16:1531. [PMID: 38794769 PMCID: PMC11124328 DOI: 10.3390/nu16101531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Several metabolites of the essential amino acid tryptophan have emerged as key players in gut homeostasis through different cellular pathways, particularly through metabolites which can activate the aryl hydrocarbon receptor (AHR). This study aimed to map the metabolism of tryptophan in early life and investigate the effects of specific metabolites on epithelial cells and barrier integrity. Twenty-one tryptophan metabolites were measured in the feces of full-term and preterm neonates as well as in human milk and formula. The ability of specific AHR metabolites to regulate cytokine-induced IL8 expression and maintain barrier integrity was assessed in Caco2 cells and human fetal organoids (HFOs). Overall, higher concentrations of tryptophan metabolites were measured in the feces of full-term neonates compared to those of preterm ones. Within AHR metabolites, indole-3-lactic acid (ILA) was significantly higher in the feces of full-term neonates. Human milk contained different levels of several tryptophan metabolites compared to formula. Particularly, within the AHR metabolites, indole-3-sulfate (I3S) and indole-3-acetic acid (IAA) were significantly higher compared to formula. Fecal-derived ILA and milk-derived IAA were capable of reducing TNFα-induced IL8 expression in Caco2 cells and HFOs in an AHR-dependent manner. Furthermore, fecal-derived ILA and milk-derived IAA significantly reduced TNFα-induced barrier disruption in HFOs.
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Affiliation(s)
- Naomi V. Wieser
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (C.V.); (W.J.d.J.)
| | - Mohammed Ghiboub
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (C.V.); (W.J.d.J.)
- Amsterdam Gastroenterology, Endocrinology, Metabolism (AGEM), 1105 AZ Amsterdam, The Netherlands;
- Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Caroline Verseijden
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (C.V.); (W.J.d.J.)
- Amsterdam Gastroenterology, Endocrinology, Metabolism (AGEM), 1105 AZ Amsterdam, The Netherlands;
| | - Johannes B. van Goudoever
- Department of Pediatrics, Emma Children’s Hospital, Dutch National Human Milk Bank, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (J.B.v.G.); (A.S.)
| | - Anne Schoonderwoerd
- Department of Pediatrics, Emma Children’s Hospital, Dutch National Human Milk Bank, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (J.B.v.G.); (A.S.)
| | - Tim G. J. de Meij
- Amsterdam Gastroenterology, Endocrinology, Metabolism (AGEM), 1105 AZ Amsterdam, The Netherlands;
- Department of Pediatric Gastroenterology, Vrije Universiteit University Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Hendrik J. Niemarkt
- Department of Neonatology, Maxima Medical Center, De Run 4600, 5504 DB Veldhoven, The Netherlands;
- Department of Electrical Engineering, Technical University Eindhoven, Groene Loper 3, 5612 AE Eindhoven, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Antoine Lefèvre
- UMR 1253, iBrain, University of Tours, Inserm, 37044 Tours, France; (A.L.); (P.E.)
| | - Patrick Emond
- UMR 1253, iBrain, University of Tours, Inserm, 37044 Tours, France; (A.L.); (P.E.)
- In Vitro Nuclear Medicine Laboratory, Regional University Hospital Center of Tours University, 37044 Tours, France
| | - Joep P. M. Derikx
- Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (C.V.); (W.J.d.J.)
- Amsterdam Gastroenterology, Endocrinology, Metabolism (AGEM), 1105 AZ Amsterdam, The Netherlands;
- Department of Surgery, University Hospital Bonn, 53113 Bonn, Germany
| | - Bruno Sovran
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (C.V.); (W.J.d.J.)
- Department of Pediatric Surgery, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
- Emma Center for Personalized Medicine, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Platnich CM, Earle MK, Keyser UF. Chemical Annealing Restructures RNA for Nanopore Detection. J Am Chem Soc 2024; 146:12919-12924. [PMID: 38691627 PMCID: PMC11099964 DOI: 10.1021/jacs.4c03753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/03/2024]
Abstract
RNA is a key biochemical marker, yet its chemical instability and complex secondary structure hamper its integration into DNA nanotechnology-based sensing platforms. Relying on the denaturation of the native RNA structure using urea, we show that restructured DNA/RNA hybrids can readily be prepared at room temperature. Using solid-state nanopore sensing, we demonstrate that the structures of our DNA/RNA hybrids conform to the design at the single-molecule level. Employing this chemical annealing procedure, we mitigate RNA self-cleavage, enabling the direct detection of restructured RNA molecules for biosensing applications.
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Affiliation(s)
- Casey M. Platnich
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Max K. Earle
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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33
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Altınönder İ, Kaya M, Yentür SP, Çakar A, Durmuş H, Yegen G, Özkan B, Parman Y, Sawalha AH, Saruhan-Direskeneli G. Thymic gene expression analysis reveals a potential link between HIF-1A and Th17/Treg imbalance in thymoma associated myasthenia gravis. J Neuroinflammation 2024; 21:126. [PMID: 38734662 PMCID: PMC11088784 DOI: 10.1186/s12974-024-03095-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/07/2024] [Indexed: 05/13/2024] Open
Abstract
Myasthenia gravis (MG) is an immune-mediated disease frequently associated with thymic changes. Increased T helper 17 (Th17) cell activity and dysfunctional regulatory T (Treg) cells have been demonstrated in subgroups of MG. On the other hand, hypoxia-inducible factor 1 (HIF-1) has been shown to regulate the Th17/Treg balance by inducing Th17 differentiation while attenuating Treg development. To identify the underlying mechanisms of different thymic pathologies in MG development, we evaluated thymic samples from thymoma-associated myasthenia gravis (TAMG), MG with hyperplasia (TFH-MG) and thymoma without MG (TOMA) patients. Differential gene expression analysis revealed that TAMG and TFH-MG cells are associated with different functional pathways. A higher RORC/FOXP3 ratio provided evidence for Th17/Treg imbalance in TAMG potentially related to increased HIF1A. The hypoxic microenvironment in thymoma may be a driver of TAMG by increasing HIF1A. These findings may lead to new therapeutic approaches targeting HIF1A in the development of TAMG.
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Affiliation(s)
- İlayda Altınönder
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Mustafa Kaya
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Sibel P Yentür
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Arman Çakar
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Hacer Durmuş
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Gülçin Yegen
- Department of Thoracic Surgery, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Berker Özkan
- Department of Pathology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Yeşim Parman
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
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Sočan V, Dolinar K, Kržan M. Kinetic Properties and Pharmacological Modulation of High- and Low-Affinity Dopamine Transport in Striatal Astrocytes of Adult Rats. Int J Mol Sci 2024; 25:5135. [PMID: 38791173 PMCID: PMC11121484 DOI: 10.3390/ijms25105135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Astrocytes actively participate in neurotransmitter homeostasis by bidirectional communication with neuronal cells, a concept named the tripartite synapse, yet their role in dopamine (DA) homeostasis remains understudied. In the present study, we investigated the kinetic and molecular mechanisms of DA transport in cultured striatal astrocytes of adult rats. Kinetic uptake experiments were performed using radiolabeled [3H]-DA, whereas mRNA expression of the dopamine, norepinephrine, organic cation and plasma membrane monoamine transporters (DAT, NET, OCTs and PMAT) and DA receptors D1 and D2 was determined by qPCR. Additionally, astrocyte cultures were subjected to a 24 h treatment with the DA receptor agonist apomorphine, the DA receptor antagonist haloperidol and the DA precursor L-DOPA. [3H]-DA uptake exhibited temperature, concentration and sodium dependence, with potent inhibition by desipramine, nortriptyline and decynium-22, suggesting the involvement of multiple transporters. qPCR revealed prominent mRNA expression of the NET, the PMAT and OCT1, alongside lower levels of mRNA for OCT2, OCT3 and the DAT. Notably, apomorphine significantly altered NET, PMAT and D1 mRNA expression, while haloperidol and L-DOPA had a modest impact. Our findings demonstrate that striatal astrocytes aid in DA clearance by multiple transporters, which are influenced by dopaminergic drugs. Our study enhances the understanding of regional DA uptake, paving the way for targeted therapeutic interventions in dopaminergic disorders.
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Affiliation(s)
- Vesna Sočan
- Institute of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Klemen Dolinar
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Mojca Kržan
- Institute of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
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35
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Yu M, Tang X, Li Z, Wang W, Wang S, Li M, Yu Q, Xie S, Zuo X, Chen C. High-throughput DNA synthesis for data storage. Chem Soc Rev 2024; 53:4463-4489. [PMID: 38498347 DOI: 10.1039/d3cs00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
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Affiliation(s)
- Meng Yu
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaohui Tang
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Zhenhua Li
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Weidong Wang
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Shaopeng Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Qiuliyang Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Sijia Xie
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Chang Chen
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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36
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Waisman A, Sevlever F, Saulnier D, Francia M, Blanco R, Amín G, Lombardi A, Biani C, Palma MB, Scarafía A, Smucler J, La Greca A, Moro L, Sevlever G, Guberman A, Miriuka S. The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network. Sci Rep 2024; 14:10420. [PMID: 38710730 PMCID: PMC11074312 DOI: 10.1038/s41598-024-59247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
In the mouse embryo, the transition from the preimplantation to the postimplantation epiblast is governed by changes in the gene regulatory network (GRN) that lead to transcriptional, epigenetic, and functional changes. This transition can be faithfully recapitulated in vitro by the differentiation of mouse embryonic stem cells (mESCs) to epiblast-like cells (EpiLCs), that reside in naïve and formative states of pluripotency, respectively. However, the GRN that drives this conversion is not fully elucidated. Here we demonstrate that the transcription factor OCT6 is a key driver of this process. Firstly, we show that Oct6 is not expressed in mESCs but is rapidly induced as cells exit the naïve pluripotent state. By deleting Oct6 in mESCs, we find that knockout cells fail to acquire the typical morphological changes associated with the formative state when induced to differentiate. Additionally, the key naïve pluripotency TFs Nanog, Klf2, Nr5a2, Prdm14, and Esrrb were expressed at higher levels than in wild-type cells, indicating an incomplete dismantling of the naïve pluripotency GRN. Conversely, premature expression of Oct6 in naïve cells triggered a rapid morphological transformation mirroring differentiation, that was accompanied by the upregulation of the endogenous Oct6 as well as the formative genes Sox3, Zic2/3, Foxp1, Dnmt3A and FGF5. Strikingly, we found that OCT6 represses Nanog in a bistable manner and that this regulation is at the transcriptional level. Moreover, our findings also reveal that Oct6 is repressed by NANOG. Collectively, our results establish OCT6 as a key TF in the dissolution of the naïve pluripotent state and support a model where Oct6 and Nanog form a double negative feedback loop which could act as an important toggle mediating the transition to the formative state.
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Affiliation(s)
- Ariel Waisman
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
| | - Federico Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Denisse Saulnier
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Marcos Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Renata Blanco
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Guadalupe Amín
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Antonella Lombardi
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Celeste Biani
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - María Belén Palma
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Agustina Scarafía
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Joaquín Smucler
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandro La Greca
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Lucía Moro
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Gustavo Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Miriuka
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
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Schyma C, Müller R, Brünig J, Zieger M, Utz S, Grabmüller M. The muzzle to target distance -staining inside different parts of the firearm barrel. Int J Legal Med 2024; 138:1149-1156. [PMID: 38091066 PMCID: PMC11003904 DOI: 10.1007/s00414-023-03141-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 04/11/2024]
Abstract
Biological traces inside firearm barrels were observed as a result of contact shots to the head. The present study was conducted to investigate the influence of the muzzle to target distance on staining inside the anterior and posterior part of firearm barrels. Ninety-nine shots were fired to so-called reference cubes (10% gelatine, 12 cm edge length, embedded paint-blood-pad) using three current handguns. Shot range was varied from contact to 50 cm distance. High-speed cameras recorded external backspatter. Endoscopic examination assessed visible staining along the barrel. Each two swabbings were gathered from the anterior and the posterior part of the barrel. The first swabs were submitted to quantitative PCR, the second ones to DNA-RNA-co-extraction. Thorough mechanical and chemical cleaning was performed to avoid any contamination which was controlled by negative zero swabs after each cleaning. In single shots up to 50 cm distance, minimal, but DNA-positive sporadic traces were detected inside the barrel in vicinity of the muzzle. Visible complex staining varying in extent was observed in the anterior barrel part for 10 cm or less distance in dependence of the calibre. The posterior part showed detectable traces only after close range shots (< 5 cm). Generally staining inside the barrel decreased from the muzzle to the rear end, which correlated with the yield of DNA. Some contact shots did not cause any staining in the posterior part of the barrel despite massive external backspatter. Blood-specific miRNA was primarily found where DNA was detected. This experience encourages to take a second swab for RNA analysis. The amount of nucleic acids in the barrel at varying muzzle to target distances is subject to large variations between individual shots and therefore appears not suitable for a reliable determination of the shot distance in a particular case on its own. Instead, shot range estimation should also take into account morphology and distribution of traces inside the barrel.
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Affiliation(s)
- Christian Schyma
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland.
| | - Rolf Müller
- Criminal Investigation Service, Cantonal Police Department of Bern, Nordring 30, 3013, Bern, Switzerland
| | - Julia Brünig
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland
| | - Martin Zieger
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland
| | - Melanie Grabmüller
- Institute of Legal Medicine, University Bonn, Stiftsplatz 12, 53111, Bonn, Germany
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38
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Ahmadipour B, Kalantar M, Abaszadeh S, Hassanpour H. Antioxidant and antihyperlipidemic effects of hawthorn extract (Crataegus oxyacantha) in broiler chickens. Vet Med Sci 2024; 10:e1414. [PMID: 38504617 PMCID: PMC10951631 DOI: 10.1002/vms3.1414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND One of the main problems in the poultry industry is excess body fat, and the anti-fat effect of Cratagus extract has been confirmed in several studies. OBJECTIVES The present study was carried out to investigate the effects of hawthorn extract (Crataegus oxyacantha) on growth performance, haematological variables and hepatic gene expression in broiler chickens reared at high altitude (2100 m). METHODS A total of 225-day-old chicks (Ross 308) were randomly distributed into three treatments. Experimental treatments were prepared by adding 0.0, 0.2 and 0.4 mL of hawthorn extract per litre of consumption of water. RESULTS The results showed that weight gain and feed conversion ratio were significantly improved and abdominal fat decreased by consumption of two levels of Crateagus extract when compared to the control (p < 0.05). Consumption of hawthorn extract decreased circulatory levels of malondialdehyde, triacylglycerol, total cholesterol and low-density lipoproteins cholesterol but increased ferric reducing antioxidant power and high-density lipoproteins cholesterol (p < 0.05). Hawthorn extract caused an up-regulation of catalase, superoxide dismutase1, glutathione peroxidase1 and peroxisome proliferator-activated receptor alpha but reduced the expression of key lipogenic enzymes (p < 0.05). CONCLUSIONS Overall, consumption of 0.4 mL hawthorn extract per litre of drinking water, improved growth performance, suppressed lipogenesis and enhanced antioxidant response.
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Affiliation(s)
- Behnam Ahmadipour
- Department of Animal ScienceFaculty of AgricultureShahrekord UniversityShahrekordIran
| | - Majid Kalantar
- Department of Animal ScienceQom's Agricultural Research and Education CenterAgricultural Research, Education, and Extension Organization, Jihad‐e‐Keshavarzi MinistryQomIran
| | - Samira Abaszadeh
- Department of Animal ScienceFaculty of AgricultureShahrekord UniversityShahrekordIran
| | - Hossein Hassanpour
- Department of Basic SciencesFaculty of Veterinary MedicineShahrekord UniversityShahrekordIran
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39
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Meillère A, Buchanan KL, Eastwood JR, Mariette MM. Pre- and postnatal noise directly impairs avian development, with fitness consequences. Science 2024; 384:475-480. [PMID: 38662819 DOI: 10.1126/science.ade5868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/28/2024] [Indexed: 05/03/2024]
Abstract
Noise pollution is expanding at an unprecedented rate and is increasingly associated with impaired reproduction and development across taxa. However, whether noise sound waves are intrinsically harmful for developing young-or merely disturb parents-and the fitness consequences of early exposure remain unknown. Here, by only manipulating the offspring, we show that sole exposure to noise in early life in zebra finches has fitness consequences and causes embryonic death during exposure. Exposure to pre- and postnatal traffic noise cumulatively impaired nestling growth and physiology and aggravated telomere shortening across life stages until adulthood. Consistent with a long-term somatic impact, early life noise exposure, especially prenatally, decreased individual offspring production throughout adulthood. Our findings suggest that the effects of noise pollution are more pervasive than previously realized.
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Affiliation(s)
- Alizée Meillère
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
- Doñana Biological Station EBD-CSIC, Seville, Spain
| | - Katherine L Buchanan
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Justin R Eastwood
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Mylene M Mariette
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
- Doñana Biological Station EBD-CSIC, Seville, Spain
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40
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Bamogo P, Tiendrébéogo F, Brugidou C, Sérémé D, Djigma FW, Simporé J, Lacombe S. Rice yellow mottle virus is a suitable amplicon vector for an efficient production of an anti-leishmianiasis vaccine in Nicotiana benthamiana leaves. BMC Biotechnol 2024; 24:21. [PMID: 38658899 PMCID: PMC11044499 DOI: 10.1186/s12896-024-00851-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Since the 2000's, plants have been used as bioreactors for the transient production of molecules of interest such as vaccines. To improve protein yield, "amplicon" vectors based on plant viruses are used. These viral constructs, engineered to carry the gene of interest replicate strongly once introduced into the plant cell, allowing significant accumulation of the protein. Here, we evaluated the suitability of the monocot-infecting RNA virus Rice yellow mottle virus (RYMV) as an amplicon vector. The promastigote surface antigen (PSA) of the protozoan Leishmania was considered as a protein of interest due to its vaccine properties against canine leishmaniasis. RESULTS Since P1 (ORF1) and CP (ORF3) proteins are not strictly necessary for viral replication, ORF1 was deleted and the PSA gene was substituted to ORF3 in the RYMV-based vector. We evaluated its expression in the best described plant bioreactor system, Nicotiana benthamiana which, unlike rice, allows transient transformation by Agrobacterium. Despite not being its natural host, we demonstrated a low level of RYMV-based vector replication in N. benthamiana leaves. Under optimized ratio, we showed that the P19 silencing suppressor in combination with the missing viral CP ORF significantly enhanced RYMV amplicon replication in N. benthamiana. Under these optimized CP/P19 conditions, we showed that the RYMV amplicon replicated autonomously in the infiltrated N. benthamiana cells, but was unable to move out of the infiltrated zones. Finally, we showed that when the RYMV amplicon was expressed under the optimized conditions we set up, it allowed enhanced PSA protein accumulation in N. benthamiana compared to the PSA coding sequence driven by the 35S promoter without amplicon background. CONCLUSION This work demonstrates that a non-dicot-infecting virus can be used as an amplicon vector for the efficient production of proteins of interest such as PSA in N. benthamiana leaves.
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Affiliation(s)
- Pka Bamogo
- Institut de L'Environnement et de Recherches Agricoles (INERA), LMI Patho-Bios Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso.
- Université Joseph Ki-Zerbo, Laboratoire de biologie moléculaire et de Génétique (LABIOGENE), Ecole Doctorale Sciences et Technologie, Centre de recherche biomoléculaire Piétro Annigoni (CERBA), Ouagadougou, Burkina Faso.
- PHIM Plant Health Institute Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - F Tiendrébéogo
- Institut de L'Environnement et de Recherches Agricoles (INERA), LMI Patho-Bios Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - C Brugidou
- Université Joseph Ki-Zerbo, Laboratoire de biologie moléculaire et de Génétique (LABIOGENE), Ecole Doctorale Sciences et Technologie, Centre de recherche biomoléculaire Piétro Annigoni (CERBA), Ouagadougou, Burkina Faso
- PHIM Plant Health Institute Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - D Sérémé
- Institut de L'Environnement et de Recherches Agricoles (INERA), LMI Patho-Bios Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - F W Djigma
- Université Joseph Ki-Zerbo, Laboratoire de biologie moléculaire et de Génétique (LABIOGENE), Ecole Doctorale Sciences et Technologie, Centre de recherche biomoléculaire Piétro Annigoni (CERBA), Ouagadougou, Burkina Faso
| | - J Simporé
- Université Joseph Ki-Zerbo, Laboratoire de biologie moléculaire et de Génétique (LABIOGENE), Ecole Doctorale Sciences et Technologie, Centre de recherche biomoléculaire Piétro Annigoni (CERBA), Ouagadougou, Burkina Faso
| | - S Lacombe
- Université Joseph Ki-Zerbo, Laboratoire de biologie moléculaire et de Génétique (LABIOGENE), Ecole Doctorale Sciences et Technologie, Centre de recherche biomoléculaire Piétro Annigoni (CERBA), Ouagadougou, Burkina Faso
- PHIM Plant Health Institute Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Baudic M, Murata H, Bosada FM, Melo US, Aizawa T, Lindenbaum P, van der Maarel LE, Guedon A, Baron E, Fremy E, Foucal A, Ishikawa T, Ushinohama H, Jurgens SJ, Choi SH, Kyndt F, Le Scouarnec S, Wakker V, Thollet A, Rajalu A, Takaki T, Ohno S, Shimizu W, Horie M, Kimura T, Ellinor PT, Petit F, Dulac Y, Bru P, Boland A, Deleuze JF, Redon R, Le Marec H, Le Tourneau T, Gourraud JB, Yoshida Y, Makita N, Vieyres C, Makiyama T, Mundlos S, Christoffels VM, Probst V, Schott JJ, Barc J. TAD boundary deletion causes PITX2-related cardiac electrical and structural defects. Nat Commun 2024; 15:3380. [PMID: 38643172 PMCID: PMC11032321 DOI: 10.1038/s41467-024-47739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.
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Affiliation(s)
- Manon Baudic
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Hiroshige Murata
- The Department of Cardiovascular Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Fernanda M Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353, Berlin, Germany
| | - Takanori Aizawa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Pierre Lindenbaum
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Lieve E van der Maarel
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Amaury Guedon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Estelle Baron
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Enora Fremy
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Adrien Foucal
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Taisuke Ishikawa
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Hiroya Ushinohama
- Department of Cardiology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Florence Kyndt
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Solena Le Scouarnec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Aurélie Thollet
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Annabelle Rajalu
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Tadashi Takaki
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Takeda-CiRA Joint Program for iPS Cell Applications, Fujisawa, Japan
- Department of Pancreatic Islet Cell Transplantation, National Center for Global Health and Medicine, Tokyo, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Wataru Shimizu
- The Department of Cardiovascular Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Ohtsu, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, Hôpital Jeanne de Flandre, F-59000, Lille, France
- University of Lille, EA 7364-RADEME, F-59000, Lille, France
| | - Yves Dulac
- Unité de Cardiologie Pédiatrique, Hôpital des Enfants, F-31000, Toulouse, France
| | - Paul Bru
- Service de Cardiologie, GH La Rochelle, F-17019, La Rochelle, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Hervé Le Marec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Thierry Le Tourneau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Jean-Baptiste Gourraud
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands
| | - Yoshinori Yoshida
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Naomasa Makita
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
- Department of Cardiology, Sapporo Teishinkai Hospital, Sapporo, Japan
| | - Claude Vieyres
- Cabinet Cardiologique, Clinique St. Joseph, F-16000, Angoulême, France
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Community Medicine Supporting System, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Stephan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353, Berlin, Germany
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Vincent Probst
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands
| | - Jean-Jacques Schott
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands.
| | - Julien Barc
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands.
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Ravindran S, Underwood SL, Dorrens J, Seeker LA, Watt K, Wilbourn RV, Sparks AM, Sinclair R, Chen Z, Pilkington JG, McNeilly TN, Harrington L, Pemberton JM, Nussey DH, Froy H. No correlative evidence of costs of infection or immunity on leucocyte telomere length in a wild population of Soay sheep. Proc Biol Sci 2024; 291:20232946. [PMID: 38565156 PMCID: PMC10987235 DOI: 10.1098/rspb.2023.2946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Telomere length (TL) is a biomarker hypothesized to capture evolutionarily and ecologically important physiological costs of reproduction, infection and immunity. Few studies have estimated the relationships among infection status, immunity, TL and fitness in natural systems. The hypothesis that short telomeres predict reduced survival because they reflect costly consequences of infection and immune investment remains largely untested. Using longitudinal data from a free-living Soay sheep population, we tested whether leucocyte TL was predicted by infection with nematode parasites and antibody levels against those parasites. Helminth parasite burdens were positively associated with leucocyte TL in both lambs and adults, which is not consistent with TL reflecting infection costs. We found no association between TL and helminth-specific IgG levels in either young or old individuals which suggests TL does not reflect costs of an activated immune response or immunosenescence. Furthermore, we found no support for TL acting as a mediator of trade-offs between infection, immunity and subsequent survival in the wild. Our results suggest that while variation in TL could reflect short-term variation in resource investment or environmental conditions, it does not capture costs of infection and immunity, nor does it behave like a marker of an individual's helminth-specific antibody immune response.
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Affiliation(s)
- Sanjana Ravindran
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sarah L. Underwood
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jennifer Dorrens
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Luise A. Seeker
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kathryn Watt
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Rachael V. Wilbourn
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alexandra M. Sparks
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rona Sinclair
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Zhulin Chen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jill G. Pilkington
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada H3C 3J7
| | - Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Daniel H. Nussey
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Hannah Froy
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Nasreen M, Ellis D, Hosmer J, Essilfie AT, Fantino E, Sly P, McEwan AG, Kappler U. The DmsABC S-oxide reductase is an essential component of a novel, hypochlorite-inducible system of extracellular stress defense in Haemophilus influenzae. Front Microbiol 2024; 15:1359513. [PMID: 38638903 PMCID: PMC11024254 DOI: 10.3389/fmicb.2024.1359513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
Defenses against oxidative damage to cell components are essential for survival of bacterial pathogens during infection, and here we have uncovered that the DmsABC S-/N-oxide reductase is essential for virulence and in-host survival of the human-adapted pathogen, Haemophilus influenzae. In several different infection models, H. influenzae ΔdmsA strains showed reduced immunogenicity as well as lower levels of survival in contact with host cells. Expression of DmsABC was induced in the presence of hypochlorite and paraquat, closely linking this enzyme to defense against host-produced antimicrobials. In addition to methionine sulfoxide, DmsABC converted nicotinamide- and pyrimidine-N-oxide, precursors of NAD and pyrimidine for which H. influenzae is an auxotroph, at physiologically relevant concentrations, suggesting that these compounds could be natural substrates for DmsABC. Our data show that DmsABC forms part of a novel, periplasmic system for defense against host-induced S- and N-oxide stress that also comprises the functionally related MtsZ S-oxide reductase and the MsrAB peptide methionine sulfoxide reductase. All three enzymes are induced following exposure of the bacteria to hypochlorite. MsrAB is required for physical resistance to HOCl and protein repair. In contrast, DmsABC was required for intracellular colonization of host cells and, together with MtsZ, contributed to resistance to N-Chlorotaurine. Our work expands and redefines the physiological role of DmsABC and highlights the importance of different types of S-oxide reductases for bacterial virulence.
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Affiliation(s)
- Marufa Nasreen
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Daniel Ellis
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Jennifer Hosmer
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | | | | | - Peter Sly
- Child Health Research Centre, South Brisbane, QLD, Australia
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
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44
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Zhao X, Lv S, Li N, Zou Q, Sun L, Song T. YTHDF2 protein stabilization by the deubiquitinase OTUB1 promotes prostate cancer cell proliferation via PRSS8 mRNA degradation. J Biol Chem 2024; 300:107152. [PMID: 38462165 PMCID: PMC11002313 DOI: 10.1016/j.jbc.2024.107152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024] Open
Abstract
Prostate cancer is a leading cause of cancer-related mortality in males. Dysregulation of RNA adenine N-6 methylation (m6A) contributes to cancer malignancy. m6A on mRNA may affect mRNA splicing, turnover, transportation, and translation. m6A exerts these effects, at least partly, through dedicated m6A reader proteins, including YTH domain-containing family protein 2 (YTHDF2). YTHDF2 is necessary for development while its dysregulation is seen in various cancers, including prostate cancer. However, the mechanism underlying the dysregulation and function of YTHDF2 in cancer remains elusive. Here, we find that the deubiquitinase OUT domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) increases YTHDF2 protein stability by inhibiting its ubiquitination. With in vivo and in vitro ubiquitination assays, OTUB1 is shown to block ubiquitin transfer to YTHDF2 independent of its deubiquitinase activity. Furthermore, analysis of functional transcriptomic data and m6A-sequencing data identifies PRSS8 as a potential tumor suppressor gene. OTUB1 and YTHDF2 decrease mRNA and protein levels of PRSS8, which is a trypsin-like serine protease. Mechanistically, YTHDF2 binds PRSS8 mRNA and promotes its degradation in an m6A-dependent manner. Further functional study on cellular and mouse models reveals PRSS8 is a critical downstream effector of the OTUB1-YTHDF2 axis in prostate cancer. We find in prostate cancer cells, PRSS8 decreases nuclear β-catenin level through E-cadherin, which is independent of its protease activity. Collectively, our study uncovers a key regulator of YTHDF2 protein stability and establishes a functional OTUB1-YTHDF2-PRSS8 axis in prostate cancer.
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Affiliation(s)
- Xuefeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Neng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingli Zou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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45
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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] [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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46
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Chowdhury S, Ricafrente A, Cwiklinski K, Sais D, Dalton JP, Tran N, Donnelly S. Exploring the utility of circulating miRNAs as diagnostic biomarkers of fasciolosis. Sci Rep 2024; 14:7431. [PMID: 38548871 PMCID: PMC10978983 DOI: 10.1038/s41598-024-57704-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/21/2024] [Indexed: 04/01/2024] Open
Abstract
Effective management and control of parasitic infections on farms depends on their early detection. Traditional serological diagnostic methods for Fasciola hepatica infection in livestock are specific and sensitive, but currently the earliest detection of the parasite only occurs at approximately three weeks post-infection. At this timepoint, parasites have already entered the liver and caused the tissue damage and immunopathology that results in reduced body weight and loss in productivity. Here, we investigated whether the differential abundance of micro(mi)miRNAs in sera of F. hepatica-infected sheep has potential as a tool for the early diagnosis of infection. Using miRNA sequencing analysis, we discovered specific profiles of sheep miRNAs at both the pre-hepatic and hepatic infection phases in comparison to non-infected sheep. In addition, six F. hepatica-derived miRNAs were specifically identified in sera from infected sheep. Thus, a panel of differentially expressed miRNAs comprising four sheep (miR-3231-3p; miR133-5p; 3957-5p; 1197-3p) and two parasite miRNAs (miR-124-3p; miR-Novel-11-5p) were selected as potential biomarkers. The expression of these candidates in sera samples from longitudinal sheep infection studies collected between 7 days and 23 weeks was quantified using RT-qPCR and compared to samples from age-matched non-infected sheep. We identified oar-miR-133-5p and oar-miR-3957-5p as promising biomarkers of fasciolosis, detecting infection as early as 7 days. The differential expression of the other selected miRNAs was not sufficient to diagnose infection; however, our analysis found that the most abundant forms of fhe-miR-124-3p in sera were sequence variants (IsomiRs) of the canonical miRNA, highlighting the critical importance of primer design for accurate diagnostic RT-qPCR. Accordingly, this investigative study suggests that certain miRNAs are biomarkers of F. hepatica infection and validates miRNA-based diagnostics for the detection of fasciolosis in sheep.
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Affiliation(s)
- Sumaiya Chowdhury
- The School of Life Sciences, University of Technology, Sydney, Australia
| | - Alison Ricafrente
- The School of Life Sciences, University of Technology, Sydney, Australia
| | - Krystyna Cwiklinski
- Centre for One Health, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Dayna Sais
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - John P Dalton
- Centre for One Health, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia.
| | - Sheila Donnelly
- The School of Life Sciences, University of Technology, Sydney, Australia.
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Espenberg M, Pille K, Yang B, Maddison M, Abdalla M, Smith P, Li X, Chan PL, Mander Ü. Towards an integrated view on microbial CH 4, N 2O and N 2 cycles in brackish coastal marsh soils: A comparative analysis of two sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170641. [PMID: 38325442 PMCID: PMC10884468 DOI: 10.1016/j.scitotenv.2024.170641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.
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Affiliation(s)
- Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia; Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
| | - Kristin Pille
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Bin Yang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mohamed Abdalla
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Xiuzhen Li
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Ping-Lung Chan
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Castañón-Suárez CA, Arrizubieta M, Castelán-Muñoz N, Sánchez-Rodríguez DB, Caballero-Cordero C, Zluhan-Martínez E, Patiño-Olvera SC, Arciniega-González J, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development. FRONTIERS IN PLANT SCIENCE 2024; 15:1331269. [PMID: 38576790 PMCID: PMC10994003 DOI: 10.3389/fpls.2024.1331269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024]
Abstract
MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. By analyzing loss-of-function and overexpression lines, we found that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas SOC1 overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in xal2-2 roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.
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Affiliation(s)
- Claudio A. Castañón-Suárez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| | - Diana Belén Sánchez-Rodríguez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carolina Caballero-Cordero
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sandra C. Patiño-Olvera
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - J.Arturo Arciniega-González
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Bonnet A, Bluy L, Gress L, Canario L, Ravon L, Sécula A, Billon Y, Liaubet L. Sex and fetal genome influence gene expression in pig endometrium at the end of gestation. BMC Genomics 2024; 25:303. [PMID: 38515025 PMCID: PMC10958934 DOI: 10.1186/s12864-024-10144-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND A fine balance of feto-maternal resource allocation is required to support pregnancy, which depends on interactions between maternal and fetal genetic potential, maternal nutrition and environment, endometrial and placental functions. In particular, some imprinted genes have a role in regulating maternal-fetal nutrient exchange, but few have been documented in the endometrium. The aim of this study is to describe the expression of 42 genes, with parental expression, in the endometrium comparing two extreme breeds: Large White (LW); Meishan (MS) with contrasting neonatal mortality and maturity at two days of gestation (D90-D110). We investigated their potential contribution to fetal maturation exploring genes-fetal phenotypes relationships. Last, we hypothesized that the fetal genome and sex influence their endometrial expression. For this purpose, pure and reciprocally crossbred fetuses were produced using LW and MS breeds. Thus, in the same uterus, endometrial samples were associated with its purebred or crossbred fetuses. RESULTS Among the 22 differentially expressed genes (DEGs), 14 DEGs were differentially regulated between the two days of gestation. More gestational changes were described in LW (11 DEGs) than in MS (2 DEGs). Nine DEGs were differentially regulated between the two extreme breeds, highlighting differences in the regulation of endometrial angiogenesis, nutrient transport and energy metabolism. We identified DEGs that showed high correlations with indicators of fetal maturation, such as ponderal index at D90 and fetal blood fructose level and placental weight at D110. We pointed out for the first time the influence of fetal sex and genome on endometrial expression at D90, highlighting AMPD3, CITED1 and H19 genes. We demonstrated that fetal sex affects the expression of five imprinted genes in LW endometrium. Fetal genome influenced the expression of four genes in LW endometrium but not in MS endometrium. Interestingly, both fetal sex and fetal genome interact to influence endometrial gene expression. CONCLUSIONS These data provide evidence for some sexual dimorphism in the pregnant endometrium and for the contribution of the fetal genome to feto-maternal interactions at the end of gestation. They suggest that the paternal genome may contribute significantly to piglet survival, especially in crossbreeding production systems.
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Affiliation(s)
- Agnes Bonnet
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France.
| | - Lisa Bluy
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Laure Gress
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Laurianne Canario
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Laure Ravon
- GenESI, INRAE, Le Magneraud, 17700, Surgères, France
| | - Aurelie Sécula
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
- Present Address: IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Yvon Billon
- GenESI, INRAE, Le Magneraud, 17700, Surgères, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326, Castanet Tolosan, France
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50
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Zavallo D, Cara N, Leone M, Crescente JM, Marfil C, Masuelli R, Asurmendi S. Assessing small RNA profiles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution. PLANT CELL REPORTS 2024; 43:85. [PMID: 38453711 DOI: 10.1007/s00299-024-03170-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
KEY MESSAGE The shock produced by the allopolyploidization process on a potato interspecific diploid hybrid displays a non-random remobilization of the small RNAs profile on a variety of genomic features. Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic "shock" that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
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Affiliation(s)
- Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, 1686, Hurlingham, CP, Argentina
| | - Nicolas Cara
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Melisa Leone
- Universidad Nacional de Hurlingham, Instituto de Biotecnología, Av. Vergara 2222 (B1688GEZ), Villa Tesei, Buenos Aires, Argentina
| | - Juan Manuel Crescente
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
| | - Carlos Marfil
- Estación Experimental Agropecuaria Mendoza, Instituto Nacional de Tecnología Agropecuaria (EEA-Mendoza-INTA), San Martín 3853, Luján de Cuyo, 5534, Mendoza, Argentina
| | - Ricardo Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, 1686, Hurlingham, CP, Argentina.
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