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Yang X, Lin H, Wang M, Huang X, Li K, Xia W, Zhang Y, Wang S, Chen W, Zheng C. Identification of key genes and pathways in duck fatty liver syndrome using gene set enrichment analysis. Poult Sci 2024; 103:104015. [PMID: 39003797 PMCID: PMC11298935 DOI: 10.1016/j.psj.2024.104015] [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: 04/25/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
High-laying ducks are often fed high-energy, nutritious feeds to maintain high productivity, which predisposes them to lipid metabolism disorders and the development of fatty liver syndrome (FLS), which seriously affects production performance and has a substantial economic impact on the poultry industry. Therefore, it is necessary to elucidate the mechanisms underlying the development of fatty liver syndrome. In this study, seven Shan Partridge ducks, each with fatty liver syndrome and normal laying ducks, were selected, and Hematoxylin Eosin staining (HE staining), Masson staining, and transcriptome sequencing were performed on liver tissue. In addition to exploring key genes and pathways using conventional analysis methods, we constructed the first Kyoto Encyclopedia of Genes and Genomes (KEGG) database-based predefined gene set containing 12,764 pathways and 16,836 genes and further performed gene set enrichment analysis (GSEA) on the liver transcriptome data. Finally, key nodes and biological processes were identified via the protein-protein interaction (PPI) network. The results showed that the liver in the FL group exhibited steatosis and fibrosis, and a total of 3,663 genes with upregulated expression versus 2,296 downregulated genes were screened by conventional analysis. GSEA analysis and PPI network analysis revealed that the liver in the FL group exhibited disruption of the mitochondrial electron transport chain, leading to decreased oxidative phosphorylation and the secretion of excessive proinflammatory factors amid the continuous accumulation of lipids. Under continuous chronic inflammation, cell cycle arrest triggers apoptosis, while fibrosis becomes more severe, and procarcinogenic genes are activated, leading to the continuous development and deterioration of the liver. In conclusion, the predefined gene set constructed in this study can be used for GSEA, and the identified hub genes provide useful reference data and a solid foundation for the study of the genetic regulatory mechanism of fatty liver syndrome in ducks.
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Affiliation(s)
- Xue Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Hao Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China; College of Animal Science, Anhui Science and Technology University, Anhui 233100, P.R. China
| | - Mengpan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China; College of Animal Science & Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300391, P.R. China
| | - Xuebing Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Kaichao Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Weiguang Xia
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Yanan Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Shuang Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Wei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Chuntian Zheng
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China.
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Nilson R, Penumutchu S, Pagano FS, Belenky P. Metabolic changes associated with polysaccharide utilization reduce susceptibility to some β-lactams in Bacteroides thetaiotaomicron. mSphere 2024; 9:e0010324. [PMID: 39109911 PMCID: PMC11351048 DOI: 10.1128/msphere.00103-24] [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: 04/29/2024] [Accepted: 07/07/2024] [Indexed: 08/29/2024] Open
Abstract
Antibiotic therapy alters bacterial abundance and metabolism in the gut microbiome, leading to dysbiosis and opportunistic infections. Bacteroides thetaiotaomicron (Bth) is both a commensal in the gut and an opportunistic pathogen in other body sites. Past work has shown that Bth responds to β-lactam treatment differently depending on the metabolic environment both in vitro and in vivo. Studies of other bacteria show that an increase in respiratory metabolism independent of growth rate promotes susceptibility to bactericidal antibiotics. We propose that Bth enters a protected state linked to an increase in polysaccharide utilization and a decrease in the use of simple sugars. Here, we apply antibiotic susceptibility testing, transcriptomic analysis, and genetic manipulation to characterize this polysaccharide-mediated tolerance (PM tolerance) phenotype. We found that a variety of mono- and disaccharides increased the susceptibility of Bth to several different β-lactams compared to polysaccharides. Transcriptomics indicated a metabolic shift from reductive to oxidative branches of the tricarboxylic acid cycle on polysaccharides. Accordingly, supplementation with intermediates of central carbon metabolism had varying effects on PM tolerance. Transcriptional analysis also showed a decrease in the expression of the electron transport chain (ETC) protein NQR and an increase in the ETC protein NUO, when given fiber versus glucose. Deletion of NQR increased Bth susceptibility while deletion of NUO and a third ETC protein NDH2 had no effect. This work confirms that carbon source utilization modulates antibiotic susceptibility in Bth and that anaerobic respiratory metabolism and the ETC play an essential role.IMPORTANCEAntibiotics are indispensable medications that revolutionized modern medicine. However, their effectiveness is challenged by a large array of resistance and tolerance mechanisms. Treatment with antibiotics also disrupts the gut microbiome which can adversely affect health. Bacteroides are prevalent in the gut microbiome and yet are frequently involved in anaerobic infections. Thus, understanding how antibiotics affect these bacteria is necessary to implement proper treatment. Recent work has investigated the role of metabolism in antibiotic susceptibility in distantly related bacteria such as Escherichia coli. Using antibiotic susceptibility testing, transcriptomics, and genetic manipulation, we demonstrate that polysaccharides reduce β-lactam susceptibility when compared to monosaccharides. This finding underscores the profound impact of metabolic adaptation on the therapeutic efficacy of antibiotics. In the long term, this work indicates that modulation of metabolism could make Bacteroides more susceptible during infections or protect them in the context of the microbiome.
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Affiliation(s)
- Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Francesco S. Pagano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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Ranathunge C, Welch ME. Clinal Variation in Short Tandem Repeats Linked to Gene Expression in Sunflower ( Helianthus annuus L.). Biomolecules 2024; 14:944. [PMID: 39199332 PMCID: PMC11352406 DOI: 10.3390/biom14080944] [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: 06/24/2024] [Revised: 07/25/2024] [Accepted: 08/01/2024] [Indexed: 09/01/2024] Open
Abstract
Short tandem repeat (STR) variation is rarely explored as a contributor to adaptive evolution. An intriguing mechanism involving STRs suggests that STRs function as "tuning knobs" of adaptation whereby stepwise changes in STR allele length have stepwise effects on phenotypes. Previously, we tested the predictions of the "tuning knob" model at the gene expression level by conducting an RNA-Seq experiment on natural populations of common sunflower (Helianthus annuus L.) transecting a well-defined cline from Kansas to Oklahoma. We identified 479 STRs with significant allele length effects on gene expression (eSTRs). In this study, we expanded the range to populations further north and south of the focal populations and used a targeted approach to study the relationship between STR allele length and gene expression in five selected eSTRs. Seeds from 96 individuals from six natural populations of sunflower from Nebraska and Texas were grown in a common garden. The individuals were genotyped at the five eSTRs, and gene expression was quantified with qRT-PCR. Linear regression models identified that eSTR length in comp26672 was significantly correlated with gene expression. Further, the length of comp26672 eSTR was significantly correlated with latitude across the range from Nebraska to Texas. The eSTR locus comp26672 was located in the CHUP1 gene, a gene associated with chloroplast movement in response to light intensity, which suggests a potential adaptive role for the eSTR locus. Collectively, our results from this targeted study show a consistent relationship between allele length and gene expression in some eSTRs across a broad geographical range in sunflower and suggest that some eSTRs may contribute to adaptive traits in common sunflower.
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Gamboa M, Gotoh Y, Doloiras-Laraño A, Watanabe K. Response of wild aquatic insect communities to thermal variation through comparative landscape transcriptomics. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 116:e22137. [PMID: 39137227 DOI: 10.1002/arch.22137] [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: 06/13/2024] [Revised: 07/07/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024]
Abstract
Fluctuations in temperature are recognized as a potent driver of selection pressure, fostering genomic variations that are crucial for the adaptation and survival of organisms under selection. Notably, water temperature is a pivotal factor influencing aquatic organism persistence. By comprehending how aquatic organisms respond to shifts in water temperature, we can understand their potential physiological adaptations to environmental change in one or multiple species. This, in turn, contributes to the formulation of biologically relevant guidelines for the landscape scale transcriptome profile of organisms in lotic systems. Here, we investigated the distinct responses of seven stream stonefly species, collected from four geographical regions across Japan, to variations in temperature, including atmospheric and water temperatures. We achieved this by assessing the differences in gene expression through RNA-sequencing within individual species and exploring the patterns of community-genes among different species. We identified 735 genes that exhibited differential expressions across the temperature gradient. Remarkably, the community displayed expression levels differences of respiration and metabolic genes. Additionally, the diversity in molecular functions appeared to be linked to spatial variation, with water temperature differences potentially contributing to the overall functional diversity of genes. We found 22 community-genes with consistent expression patterns among species in response to water temperature variations. These genes related to respiration, metabolism and development exhibited a clear gradient providing robust evidence of divergent adaptive responses to water temperature. Our findings underscore the differential adaptation of stonefly species to local environmental conditions, suggesting that shared responses in gene expression may occur across multiple species under similar environmental conditions. This study emphasizes the significance of considering various species when assessing the impacts of environmental changes on aquatic insect communities and understanding potential mechanisms to cope with such changes.
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Affiliation(s)
- Maribet Gamboa
- Department of Ecology, Faculty of Science, Universidad Católica de la Santísima Concepción, Concepción, Chile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Yusuke Gotoh
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | | | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Ehime University, Center Marine Environmental Studies (CMES), Matsuyama, Japan
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5
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Colloca L, Mocci E, Wang Y, Massalee R, Chen S, Clark J, Johnson K, Fidalgo GMP, Wilson GM, Goldman D, Dorsey SG. Transcriptomic Profiles Associated with Experimental Placebo Effects in Chronic Pain. Clin Pharmacol Ther 2024; 116:380-389. [PMID: 38711244 PMCID: PMC11251865 DOI: 10.1002/cpt.3286] [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: 12/21/2023] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
Gene expression networks associated with placebo effects are understudied; in this study, we identified transcriptomic profiles associated with placebo responsivity. Participants suffering from chronic pain underwent a verbal suggestion and conditioning paradigm with individually tailored thermal painful stimulations to elicit conditioned placebo effects. Participants reported pain intensity on a visual analog scale (VAS) anchored from zero = no pain to 100 = maximum imaginable pain. RNA was extracted from venous blood and RNA sequencing and validation tests were performed to identify differentially expressed genes (DEGs) associated with placebo effects, controlling for sex and level of pain. Unbiased enrichment analyses were performed to identify biological processes associated with placebo effects. Of the 10,700 protein-coding genes that passed quality control filters, 667 were found to be associated with placebo effects (FDR <0.05). Most genes (97%) upregulated were associated with larger placebo effects. The 17 top transcriptome-wide significant genes were further validated via RT-qPCR in an independent cohort of chronic pain participants. Six of them (CCDC85B, FBXL15, HAGH, PI3, SELENOM, and TNFRSF4) showed positive and significant (P < 0.05) correlation with placebo effects in the cohort. The overall DEGs were highly enriched in regulation of expression of SLITs and ROBOs (R-HSA-9010553, FDR = 1.26e-33), metabolism of RNA (R-HSA-8953854, FDR = 1.34e-30), Huntington's disease (hsa05016, FDR = 9.84e-31), and ribosome biogenesis (GO:0042254, FDR = 2.67e-15); alternations in these pathways might jeopardize the proneness to elicit placebo effects. Future studies are needed to replicate this finding and better understand the unique molecular dynamics of people who are more or less affected by pain and placebo.
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Affiliation(s)
- Luana Colloca
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Department of Anesthesiology, School of Medicine, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, US
| | - Evelina Mocci
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
| | - Yang Wang
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, US
| | - Rachel Massalee
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
| | - Shuo Chen
- Maryland Psychiatry Research Center, School of Medicine, Baltimore, US
| | - Jewel Clark
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
| | - Kesha Johnson
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
| | - Gloria M. Patron Fidalgo
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, US
| | - Gerald M. Wilson
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, US
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism (NIAAA), NIH, Rockville, MD 20855, US
| | - Susan G. Dorsey
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, US
- Department of Anesthesiology, School of Medicine, University of Maryland, Baltimore, US
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, US
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Vilarrasa-Blasi J, Vellosillo T, Jinkerson RE, Fauser F, Xiang T, Minkoff BB, Wang L, Kniazev K, Guzman M, Osaki J, Barrett-Wilt GA, Sussman MR, Jonikas MC, Dinneny JR. Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments. Nat Commun 2024; 15:5988. [PMID: 39013881 PMCID: PMC11252407 DOI: 10.1038/s41467-024-49844-3] [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: 10/19/2022] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
Maintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the single-celled green alga Chlamydomonas reinhardtii to establish a foundational understanding of osmotic-stress signaling pathways through transcriptomics, phosphoproteomics, and functional genomics approaches. Comparison of pathways identified through these analyses with yeast and Arabidopsis allows us to infer their evolutionary conservation and divergence across these lineages. 76 genes, acting across diverse cellular compartments, were found to be important for osmotic-stress tolerance in Chlamydomonas through their functions in cytoskeletal organization, potassium transport, vesicle trafficking, mitogen-activated protein kinase and chloroplast signaling. We show that homologs for five of these genes have conserved functions in stress tolerance in Arabidopsis and reveal a novel PROFILIN-dependent stage of acclimation affecting the actin cytoskeleton that ensures tissue integrity upon osmotic stress. This study highlights the conservation of the stress response in algae and land plants, and establishes Chlamydomonas as a unicellular plant model system to dissect the osmotic stress signaling pathway.
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Affiliation(s)
- Josep Vilarrasa-Blasi
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Robert E Jinkerson
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Friedrich Fauser
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tingting Xiang
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomics Science Innovation, University of Wisconsin, Madison, WI, 53706, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Guzman
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Jacqueline Osaki
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | | | - Michael R Sussman
- Department of Biochemistry and Center for Genomics Science Innovation, University of Wisconsin, Madison, WI, 53706, USA
| | - Martin C Jonikas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA.
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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [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: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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Chapman LR, Ramnarine IVP, Zemke D, Majid A, Bell SM. Gene Expression Studies in Down Syndrome: What Do They Tell Us about Disease Phenotypes? Int J Mol Sci 2024; 25:2968. [PMID: 38474215 DOI: 10.3390/ijms25052968] [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: 02/04/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Down syndrome is a well-studied aneuploidy condition in humans, which is associated with various disease phenotypes including cardiovascular, neurological, haematological and immunological disease processes. This review paper aims to discuss the research conducted on gene expression studies during fetal development. A descriptive review was conducted, encompassing all papers published on the PubMed database between September 1960 and September 2022. We found that in amniotic fluid, certain genes such as COL6A1 and DSCR1 were found to be affected, resulting in phenotypical craniofacial changes. Additionally, other genes such as GSTT1, CLIC6, ITGB2, C21orf67, C21orf86 and RUNX1 were also identified to be affected in the amniotic fluid. In the placenta, dysregulation of genes like MEST, SNF1LK and LOX was observed, which in turn affected nervous system development. In the brain, dysregulation of genes DYRK1A, DNMT3L, DNMT3B, TBX1, olig2 and AQP4 has been shown to contribute to intellectual disability. In the cardiac tissues, dysregulated expression of genes GART, ETS2 and ERG was found to cause abnormalities. Furthermore, dysregulation of XIST, RUNX1, SON, ERG and STAT1 was observed, contributing to myeloproliferative disorders. Understanding the differential expression of genes provides insights into the genetic consequences of DS. A better understanding of these processes could potentially pave the way for the development of genetic and pharmacological therapies.
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Affiliation(s)
- Laura R Chapman
- Sheffield Children's NHS Foundation Trust, Clarkson St, Sheffield S10 2TH, UK
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
| | - Isabela V P Ramnarine
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
| | - Dan Zemke
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
| | - Arshad Majid
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2GJ, UK
| | - Simon M Bell
- Sheffield Institute of Translational Neuroscience, University of Sheffield, Glossop Road, Sheffield S10 2GF, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2GJ, UK
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9
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Shin TH, Lee G. Reduced lysosomal activity and increased amyloid beta accumulation in silica-coated magnetic nanoparticles-treated microglia. Arch Toxicol 2024; 98:121-134. [PMID: 37798515 DOI: 10.1007/s00204-023-03612-2] [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: 08/02/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
Nanoparticles have been used in neurological research in recent years because of their blood-brain barrier penetration activity. However, their potential neuronanotoxicity remains a concern. In particular, microglia, which are resident phagocytic cells, are mainly exposed to nanoparticles in the brain. We investigated the changes in lysosomal function in silica-coated magnetic nanoparticles containing rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)]-treated BV2 murine microglial cells. In addition, we analyzed amyloid beta (Aβ) accumulation and molecular changes through the integration of transcriptomics, proteomics, and metabolomics (triple-omics) analyses. Aβ accumulation significantly increased in the 0.1 μg/μl MNPs@SiO2(RITC)-treated BV2 cells compared to the untreated control and 0.01 μg/μl MNPs@SiO2(RITC)-treated BV2 cells. Moreover, the MNPs@SiO2(RITC)-treated BV2 cells showed lysosomal swelling, a dose-dependent reduction in proteolytic activity, and an increase in lysosomal swelling- and autophagy-related protein levels. Moreover, proteasome activity decreased in the MNPs@SiO2(RITC)-treated BV2 cells, followed by a concomitant reduction in intracellular adenosine triphosphate (ATP). By employing triple-omics and a machine learning algorithm, we generated an integrated single molecular network including reactive oxygen species (ROS), autophagy, lysosomal storage disease, and amyloidosis. In silico analysis of the single triple omics network predicted an increase in ROS, suppression of autophagy, and aggravation of lysosomal storage disease and amyloidosis in the MNPs@SiO2(RITC)-treated BV2 cells. Aβ accumulation and lysosomal swelling in the cells were alleviated by co-treatment with glutathione (GSH) and citrate. These findings suggest that MNPs@SiO2(RITC)-induced reduction in lysosomal activity and proteasomes can be recovered by GSH and citrate treatment. These results also highlight the relationship between nanotoxicity and Aβ accumulation.
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Affiliation(s)
- Tae Hwan Shin
- Department of Biomedical Sciences, Dong-A University, Busan, 49315, Republic of Korea.
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea.
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
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10
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Elowe CR, Babbitt C, Gerson AR. White-throated sparrow ( Zonotrichia albicollis) liver and pectoralis flight muscle transcriptomic changes in preparation for migration. Physiol Genomics 2023; 55:544-556. [PMID: 37694280 DOI: 10.1152/physiolgenomics.00018.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/03/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023] Open
Abstract
Migratory songbirds undertake challenging journeys to reach their breeding grounds each spring. They accomplish these nonstop flapping feats of endurance through a suite of physiological changes, including the development of substantial fat stores and flight muscle hypertrophy and an increased capacity for fat catabolism. In addition, migratory birds may show large reductions in organ masses during flight, including the flight muscle and liver, which they must rapidly rebuild during their migratory stopover before replenishing their fat stores. However, the molecular basis of this capacity for rapid tissue remodeling and energetic output has not been thoroughly investigated. We performed RNA-sequencing analysis of the liver and pectoralis flight muscle of captive white-throated sparrows in experimentally photostimulated migratory and nonmigratory condition to explore the mechanisms of seasonal change to metabolism and tissue mass regulation that may facilitate these migratory journeys. Based on transcriptional changes, we propose that tissue-specific adjustments in preparation for migration may alleviate the damaging effects of long-duration activity, including a potential increase to the inflammatory response in the muscle. Furthermore, we hypothesize that seasonal hypertrophy balances satellite cell recruitment and apoptosis, while little evidence appeared in the transcriptome to support myostatin-, insulin-like growth factor 1-, and mammalian target of rapamycin-mediated pathways for muscle growth. These findings can encourage more targeted molecular studies on the unique integration of pathways that we find in the development of the migratory endurance phenotype in songbirds.NEW & NOTEWORTHY Migratory songbirds undergo significant physiological changes to accomplish their impressive migratory journeys. However, we have a limited understanding of the regulatory mechanisms underlying these changes. Here, we explore the transcriptomic changes to the flight muscle and liver of white-throated sparrows as they develop the migratory condition. We use these patterns to develop hypotheses about metabolic flexibility and tissue restructuring in preparation for migration.
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Affiliation(s)
- Cory R Elowe
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States
| | - Courtney Babbitt
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States
| | - Alexander R Gerson
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States
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11
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Shivappagowda Kruthika H, Srikanta Rukmangada M, Girish Naik V. Genome size, chromosome number variation and its correlation with stomatal characters for assessment of ploidy levels in a core subset of mulberry (Morus spp.) germplasm. Gene 2023:147637. [PMID: 37442306 DOI: 10.1016/j.gene.2023.147637] [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: 04/06/2023] [Revised: 06/15/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
The large size of the germplasm collection along with scanty information on their cytological and genome constitution have hindered well-planned breeding schemes in mulberry. To address the issue, a study was undertaken to investigate the variability in DNA content and genome size, chromosome number, ploidy and its relation with important stomatal characteristics among 162 mulberry germplasm. These germplasm comprise a core subset of 150 collections along with a representative collection of different mulberry species including the wild. Among the germplasm belonging to 16 species, we identified 122 diploids (2n = 28), 4 aneuploids (2n = 30), 13 triploids (2n = 42), 15 tetraploids (2n = 56), 7 hexaploids (2n = 84) and 1 dodecosaploid (2n = 308) based on the chromosome count. Most of the cultivated mulberries are found to be diploids. The mean nuclear 2C DNA content estimated by Flow cytometry, varied from 0.723±0.006 pg (M. australis, 2n = 2x) to 7.732 pg (M. nigra, 2n = 22x). The 2C DNA content positively correlated with the ploidy status and stomatal length (r = 0.814, p<0.001). Based on the 1Cx value, the study also suggests that the majority of the polyploid species have experienced genome downsizing in relation to their diploid progenitors. This study provides the most essential information on chromosome number, ploidy and DNA content to facilitate the utilization of a core subset of germplasm in the mulberry breeding program.
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Affiliation(s)
- Hampapura Shivappagowda Kruthika
- Molecular Biology Laboratory - 1, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysuru - 570 008, India
| | - Martikyathnahalli Srikanta Rukmangada
- Molecular Biology Laboratory - 1, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysuru - 570 008, India; Department of Plant Sciences, UC Davis, California, 95616, USA
| | - Vorkady Girish Naik
- Molecular Biology Laboratory - 1, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysuru - 570 008, India.
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12
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Fangma Y, Liu M, Liao J, Chen Z, Zheng Y. Dissecting the brain with spatially resolved multi-omics. J Pharm Anal 2023; 13:694-710. [PMID: 37577383 PMCID: PMC10422112 DOI: 10.1016/j.jpha.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
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Affiliation(s)
- Yijia Fangma
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Mengting Liu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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13
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Kreitsberg R, Nääb L, Meitern R, Carbillet J, Fort J, Giraudeau M, Sepp T. The effect of environmental pollution on gene expression of seabirds: A review. MARINE ENVIRONMENTAL RESEARCH 2023; 189:106067. [PMID: 37393763 DOI: 10.1016/j.marenvres.2023.106067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
One of the biggest challenges for ecotoxicologists is to detect harmful effects of contaminants on individual organisms before they have caused significant harm to natural populations. One possible approach for discovering sub-lethal, negative health effects of pollutants is to study gene expression, to identify metabolic pathways and physiological processes affected by contaminants. Seabirds are essential components of ecosystems but highly threatened by environmental changes. Being at the top of the food chain and exhibiting a slow pace of life, they are highly exposed to contaminants and to their ultimate impacts on populations. Here we provide an overview of the currently available seabird-related gene expression studies in the context of environmental pollution. We show that studies conducted, so far, mainly focus on a small selection of xenobiotic metabolism genes, often using lethal sampling protocols, while the greater promise of gene expression studies for wild species may lie in non-invasive procedures focusing on a wider range of physiological processes. However, as whole genome approaches might still be too expensive for large-scale assessments, we also bring out the most promising candidate biomarker genes for future studies. Based on the biased geographical representativeness of the current literature, we suggest expanding studies to temperate and tropical latitudes and urban environments. Also, as links with fitness traits are very rare in the current literature, but would be highly relevant for regulatory purposes, we point to an urgent need for establishing long-term monitoring programs in seabirds that would link pollutant exposure and gene expression to fitness traits.
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Affiliation(s)
- Randel Kreitsberg
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia.
| | - Lisanne Nääb
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Richard Meitern
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Jeffrey Carbillet
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Mathieu Giraudeau
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Tuul Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
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14
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Windster JD, Sacchetti A, Schaaf GJ, Bindels EM, Hofstra RM, Wijnen RM, Sloots CE, Alves MM. A combinatorial panel for flow cytometry-based isolation of enteric nervous system cells from human intestine. EMBO Rep 2023; 24:e55789. [PMID: 36852936 PMCID: PMC10074091 DOI: 10.15252/embr.202255789] [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: 07/14/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Efficient isolation of neurons and glia from the human enteric nervous system (ENS) is challenging because of their rare and fragile nature. Here, we describe a staining panel to enrich ENS cells from the human intestine by fluorescence-activated cell sorting (FACS). We find that CD56/CD90/CD24 co-expression labels ENS cells with higher specificity and resolution than previous methods. Surprisingly, neuronal (CD24, TUBB3) and glial (SOX10) selective markers appear co-expressed by all ENS cells. We demonstrate that this contradictory staining pattern is mainly driven by neuronal fragments, either free or attached to glial cells, which are the most abundant cell types. Live neurons can be enriched by the highest CD24 and CD90 levels. By applying our protocol to isolate ENS cells for single-cell RNA sequencing, we show that these cells can be obtained with high quality, enabling interrogation of the human ENS transcriptome. Taken together, we present a selective FACS protocol that allows enrichment and discrimination of human ENS cells, opening up new avenues to study this complex system in health and disease.
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Affiliation(s)
- Jonathan D Windster
- Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Andrea Sacchetti
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerben J Schaaf
- Department of Clinical Genetics, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eric Mj Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Robert Mw Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rene Mh Wijnen
- Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Cornelius Ej Sloots
- Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands
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15
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Auger L, Bouslama S, Deschamps MH, Vandenberg G, Derome N. Absence of microbiome triggers extensive changes in the transcriptional profile of Hermetia illucens during larval ontology. Sci Rep 2023; 13:2396. [PMID: 36765081 PMCID: PMC9918496 DOI: 10.1038/s41598-023-29658-x] [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: 09/13/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Black soldier fly larvae (BSF, Hermetia illucens) have gained much attention for their industrial use as biowaste recyclers and as a new source of animal proteins. The functional effect that microbiota has on insect health and growth performance remains largely unknown. This study clarifies the role of microbiota in BSF ontogeny by investigating the differential genomic expression of BSF larvae in axenic conditions (i.e., germfree) relative to non-axenic (conventional) conditions. We used RNA-seq to measure differentially expressed transcripts between axenic and conventional condition using DESeq2 at day 4, 12 and 20 post-hatching. Gene expression was significantly up or down-regulated for 2476 transcripts mapped in gene ontology functions, and axenic larvae exhibited higher rate of down-regulated functions. Up-regulated microbiota-dependant transcriptional gene modules included the immune system, the lipid metabolism, and the nervous system. Expression profile showed a shift in late larvae (day 12 and 20), exposing a significant temporal effect on gene expression. These results provide the first evidence of host functional genes regulated by microbiota in the BSF larva, further demonstrating the importance of host-microbiota interactions on host ontology and health. These results open the door to optimization of zootechnical properties in alternative animal protein production, biowaste revalorization and recycling.
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Affiliation(s)
- Laurence Auger
- Département de Biologie, Université Laval, Quebec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Quebec, QC, Canada.
| | - Sidki Bouslama
- Département de Biologie, Université Laval, Quebec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Quebec, QC, Canada
| | | | - Grant Vandenberg
- Département des Sciences Animales, Université Laval, Quebec, QC, Canada
| | - Nicolas Derome
- Département de Biologie, Université Laval, Quebec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Quebec, QC, Canada
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16
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Carney TD, Hebalkar RY, Edeleva E, Çiçek IÖ, Shcherbata HR. Signaling through the dystrophin glycoprotein complex affects the stress-dependent transcriptome in Drosophila. Dis Model Mech 2023; 16:286223. [PMID: 36594281 PMCID: PMC9922874 DOI: 10.1242/dmm.049862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
Deficiencies in the human dystrophin glycoprotein complex (DGC), which links the extracellular matrix with the intracellular cytoskeleton, cause muscular dystrophies, a group of incurable disorders associated with heterogeneous muscle, brain and eye abnormalities. Stresses such as nutrient deprivation and aging cause muscle wasting, which can be exacerbated by reduced levels of the DGC in membranes, the integrity of which is vital for muscle health and function. Moreover, the DGC operates in multiple signaling pathways, demonstrating an important function in gene expression regulation. To advance disease diagnostics and treatment strategies, we strive to understand the genetic pathways that are perturbed by DGC mutations. Here, we utilized a Drosophila model to investigate the transcriptomic changes in mutants of four DGC components under temperature and metabolic stress. We identified DGC-dependent genes, stress-dependent genes and genes dependent on the DGC for a proper stress response, confirming a novel function of the DGC in stress-response signaling. This perspective yields new insights into the etiology of muscular dystrophy symptoms, possible treatment directions and a better understanding of DGC signaling and regulation under normal and stress conditions.
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Affiliation(s)
- Travis D. Carney
- Hannover Medical School, Research Group Gene Expression and Signaling, Institute of Cell Biochemistry, Hannover 30625, Germany,Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Rucha Y. Hebalkar
- Hannover Medical School, Research Group Gene Expression and Signaling, Institute of Cell Biochemistry, Hannover 30625, Germany
| | | | | | - Halyna R. Shcherbata
- Hannover Medical School, Research Group Gene Expression and Signaling, Institute of Cell Biochemistry, Hannover 30625, Germany,Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA,Author for correspondence ()
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17
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Priscilla L, Malathi E, Moses Inbaraj R. Sex steroid profile during oocyte development and maturation in the intertidal worm Marphysa madrasi (Polychaeta: Eunicidae) from the east coast of India. Gen Comp Endocrinol 2023; 331:114118. [PMID: 36037874 DOI: 10.1016/j.ygcen.2022.114118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Marphysa madrasi is a commercially valuable maturation diet in crustacean aquaculture. This study presents the first detailed investigation of oogenesis in the intertidal polychaete worm M. madrasi and reports the steroid profile during oocyte growth and development. Oogenesis is extraovarian type I, originating from coelomic epithelial cells, with four stages of development - primary growth, early vitellogenic, late vitellogenic, and maturation. The primary growth phase contains oogonial cells and previtellogenic oocyte clusters in the early, mid, and late stages of development form a dispersed ovary attached to blood vessels. The late previtellogenic oocytes detach from the ovary at the onset of vitellogenesis. The detached oocytes complete vitellogenesis and final maturation in the coelomic fluid as solitary free-floating cells without any connection with follicle cells. The worms display asynchronous reproduction with a heterogeneous population of developing oocytes. Steroid extracts from the polychaete homogenates in different stages of oogenesis were identified by HPLC and confirmed by LC-MS/MS. In M. madrasi, two vertebrate-type steroids, pregnenolone (P5) and 17α-hydroxyprogesterone (17-OHP) were detected and quantified. The P5 levels were low in immature worms but increased significantly by ∼ 8.3-fold in the previtellogenic stage and peaked during oocyte maturation. 17-OHP levels were low in immature worms but gradually increase as the oogenesis progress to the primary growth and early vitellogenic phase, with a significant increase (p < 0.001) during the late vitellogenic phase. Although an increase in the concentration of P5 and 17-OHP during vitellogenesis and maturation of oocytes points to a possible role in reproduction, the absence of other vertebrate-type steroids in the investigated polychaete signifies a plausible uptake of P5 and 17-OHP from the environment.
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Affiliation(s)
- Lyndsay Priscilla
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India; Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India
| | - E Malathi
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India
| | - R Moses Inbaraj
- Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India.
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18
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Zhao X, Wang Z, Ji X, Bu S, Fang P, Wang Y, Wang M, Yang Y, Zhang W, Leung AY, Shi P. Discrete single-cell microRNA analysis for phenotyping the heterogeneity of acute myeloid leukemia. Biomaterials 2022; 291:121869. [DOI: 10.1016/j.biomaterials.2022.121869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/28/2022]
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19
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Belanger CR, Dostert M, Blimkie TM, Lee AHY, Dhillon BK, Wu BC, Akhoundsadegh N, Rahanjam N, Castillo-Arnemann J, Falsafi R, Pletzer D, Haney CH, Hancock REW. Surviving the host: Microbial metabolic genes required for growth of Pseudomonas aeruginosa in physiologically-relevant conditions. Front Microbiol 2022; 13:1055512. [PMID: 36504765 PMCID: PMC9732424 DOI: 10.3389/fmicb.2022.1055512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Pseudomonas aeruginosa, like other pathogens, adapts to the limiting nutritional environment of the host by altering patterns of gene expression and utilizing alternative pathways required for survival. Understanding the genes essential for survival in the host gives insight into pathways that this organism requires during infection and has the potential to identify better ways to treat infections. Here, we used a saturated transposon insertion mutant pool of P. aeruginosa strain PAO1 and transposon insertion sequencing (Tn-Seq), to identify genes conditionally important for survival under conditions mimicking the environment of a nosocomial infection. Conditions tested included tissue culture medium with and without human serum, a murine abscess model, and a human skin organoid model. Genes known to be upregulated during infections, as well as those involved in nucleotide metabolism, and cobalamin (vitamin B12) biosynthesis, etc., were required for survival in vivo- and in host mimicking conditions, but not in nutrient rich lab medium, Mueller Hinton broth (MHB). Correspondingly, mutants in genes encoding proteins of nucleotide and cobalamin metabolism pathways were shown to have growth defects under physiologically-relevant media conditions, in vivo, and in vivo-like models, and were downregulated in expression under these conditions, when compared to MHB. This study provides evidence for the relevance of studying P. aeruginosa fitness in physiologically-relevant host mimicking conditions and identified metabolic pathways that represent potential novel targets for alternative therapies.
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Affiliation(s)
- Corrie R. Belanger
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melanie Dostert
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Travis M. Blimkie
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bhavjinder Kaur Dhillon
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Bing Catherine Wu
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Noushin Akhoundsadegh
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Negin Rahanjam
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Javier Castillo-Arnemann
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Reza Falsafi
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Pletzer
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cara H. Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,*Correspondence: Robert E. W. Hancock,
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20
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Taugbøl A, Solbakken MH, Jakobsen KS, Vøllestad LA. Salinity-induced transcriptome profiles in marine and freshwater threespine stickleback after an abrupt 6-hour exposure. Ecol Evol 2022; 12:e9395. [PMID: 36311407 PMCID: PMC9596333 DOI: 10.1002/ece3.9395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Saltwater and freshwater environments have opposing physiological challenges, yet, there are fish species that are able to enter both habitats during short time spans, and as individuals they must therefore adjust quickly to osmoregulatory contrasts. In this study, we conducted an experiment to test for plastic responses to abrupt salinity changes in two populations of threespine stickleback, Gasterosteus aculeatus, representing two ecotypes (freshwater and ancestral saltwater). We exposed both ecotypes to abrupt native (control treatment) and non-native salinities (0‰ and 30‰) and sampled gill tissue for transcriptomic analyses after 6 h of exposure. To investigate genomic responses to salinity, we analyzed four different comparisons; one for each ecotype (in their control and exposure salinity; (1) and (2), one between ecotypes in their control salinity (3), and the fourth comparison included all transcripts identified in (3) that did not show any expressional changes within ecotype in either the control or the exposed salinity (4)). Abrupt salinity transfer affected the expression of 10 and 1530 transcripts for the saltwater and freshwater ecotype, respectively, and 1314 were differentially expressed between the controls, including 502 that were not affected by salinity within ecotype (fixed expression). In total, these results indicate that factors other than genomic expressional plasticity are important for osmoregulation in stickleback, due to the need for opposite physiological pathways to survive the abrupt change in salinity.
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Affiliation(s)
- Annette Taugbøl
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
- Norwegian Institute for Nature Research (NINA)LillehammerNorway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| | - Kjetill S. Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
| | - Leif Asbjørn Vøllestad
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernNorway
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21
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Hu M, Li M, Miao M, Zhang T. Engineering Escherichia coli for the High-Titer Biosynthesis of Lacto- N-tetraose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8704-8712. [PMID: 35731707 DOI: 10.1021/acs.jafc.2c02423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lacto-N-tetraose (LNT), a member of the human milk oligosaccharides family, has received widespread attention because of its importance in infant health. We constructed a whole-cell biotransformation method in Escherichia coli BL21(DE3) for high-titer LNT synthesis. The approach was performed by using a systematic design and metabolic engineering based on the metabolic pathway of LNT. The lgtA (encoding β-1,3-N-acetylglucosaminyltransferase) and wbgO (encoding β-1,3-galactosyltransferase) genes were introduced into the engineered E. coli BL21(DE3) to construct an LNT-producing starting strain B1 (0.22 g/L). Then, the genes related to the LNT metabolic pathway were screened in two vectors to evaluate LNT synthesis. The lgtA-wbgO and galE-galT-galK genes were overexpressed through the two-plasmid system in E. coli BL21(DE3). The titer of LNT (3.42 g/L) had a gain of 14.55 times compared with that of B1. Furthermore, the ugd gene, which was associated with the UDP-Gal bypass pathway, was inactivated to further improve LNT production in shake-flask cultivation (4.14 g/L). The final fed-batch cultivation of the engineered strain produced 31.56 g/L of LNT. This study provided a strategy for the effective production of LNT in E. coli.
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Affiliation(s)
- Miaomiao Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, China
| | - Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, China
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22
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Strzepek RF, Nunn BL, Bach LT, Berges JA, Young EB, Boyd PW. The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry? JOURNAL OF PLANKTON RESEARCH 2022; 44:485-495. [PMID: 35898813 PMCID: PMC9310281 DOI: 10.1093/plankt/fbac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/05/2022] [Indexed: 05/16/2023]
Abstract
The necessity to understand the influence of global ocean change on biota has exposed wide-ranging gaps in our knowledge of the fundamental principles that underpin marine life. Concurrently, physiological research has stagnated, in part driven by the advent and rapid evolution of molecular biological techniques, such that they now influence all lines of enquiry in biological oceanography. This dominance has led to an implicit assumption that physiology is outmoded, and advocacy that ecological and biogeochemical models can be directly informed by omics. However, the main modeling currencies are biological rates and biogeochemical fluxes. Here, we ask: how do we translate the wealth of information on physiological potential from omics-based studies to quantifiable physiological rates and, ultimately, to biogeochemical fluxes? Based on the trajectory of the state-of-the-art in biomedical sciences, along with case-studies from ocean sciences, we conclude that it is unlikely that omics can provide such rates in the coming decade. Thus, while physiological rates will continue to be central to providing projections of global change biology, we must revisit the metrics we rely upon. We advocate for the co-design of a new generation of rate measurements that better link the benefits of omics and physiology.
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Affiliation(s)
- Robert F Strzepek
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS 7004, Australia
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Foege Building S113 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Lennart T Bach
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
| | - John A Berges
- Department of Biological Sciences and School of Freshwater Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Erica B Young
- Department of Biological Sciences and School of Freshwater Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Philip W Boyd
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS 7004, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
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23
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Le Luyer J, Monaco CJ, Milhade L, Reisser C, Soyez C, Raapoto H, Belliard C, Le Moullac G, Ky C, Pernet F. Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species. J Anim Ecol 2022; 91:1196-1208. [DOI: 10.1111/1365-2656.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/07/2022] [Indexed: 10/18/2022]
Affiliation(s)
- J. Le Luyer
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - C. J. Monaco
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - L. Milhade
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - C. Reisser
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD Montpellier France
| | - C. Soyez
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - H. Raapoto
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - C. Belliard
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - G. Le Moullac
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
| | - C.‐L. Ky
- Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO, F‐98719 Taravao, Tahiti, Polynésie française France
- Ifremer, IHPE, Univ. Montpellier, CNRS, Univ. Perpignan Via Domitia Montpellier France
| | - F. Pernet
- Univ Brest, Ifremer, CNRS, IRD, LEMAR, F‐29280 Plouzané France
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24
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Dion-Albert L, Bandeira Binder L, Daigle B, Hong-Minh A, Lebel M, Menard C. Sex differences in the blood-brain barrier: Implications for mental health. Front Neuroendocrinol 2022; 65:100989. [PMID: 35271863 DOI: 10.1016/j.yfrne.2022.100989] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/07/2022] [Accepted: 02/19/2022] [Indexed: 12/13/2022]
Abstract
Prevalence of mental disorders, including major depressive disorder (MDD), bipolar disorder (BD) and schizophrenia (SZ) are increasing at alarming rates in our societies. Growing evidence points toward major sex differences in these conditions, and high rates of treatment resistance support the need to consider novel biological mechanisms outside of neuronal function to gain mechanistic insights that could lead to innovative therapies. Blood-brain barrier alterations have been reported in MDD, BD and SZ. Here, we provide an overview of sex-specific immune, endocrine, vascular and transcriptional-mediated changes that could affect neurovascular integrity and possibly contribute to the pathogenesis of mental disorders. We also identify pitfalls in current literature and highlight promising vascular biomarkers. Better understanding of how these adaptations can contribute to mental health status is essential not only in the context of MDD, BD and SZ but also cardiovascular diseases and stroke which are associated with higher prevalence of these conditions.
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Affiliation(s)
- Laurence Dion-Albert
- Department of Psychiatry and Neuroscience, Faculty of Medicine and CERVO Brain Research Center, Université Laval, Quebec City, Canada
| | - Luisa Bandeira Binder
- Department of Psychiatry and Neuroscience, Faculty of Medicine and CERVO Brain Research Center, Université Laval, Quebec City, Canada
| | - Beatrice Daigle
- Department of Psychiatry and Neuroscience, Faculty of Medicine and CERVO Brain Research Center, Université Laval, Quebec City, Canada
| | - Amandine Hong-Minh
- Smurfit Institute of Genetics, Trinity College Dublin, Lincoln Place Gate, Dublin 2, Ireland
| | - Manon Lebel
- Department of Psychiatry and Neuroscience, Faculty of Medicine and CERVO Brain Research Center, Université Laval, Quebec City, Canada
| | - Caroline Menard
- Department of Psychiatry and Neuroscience, Faculty of Medicine and CERVO Brain Research Center, Université Laval, Quebec City, Canada.
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Abstract
Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.
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26
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Song J, Austin JD, Yang H. Comparative Transcriptomics of the Northern Quahog Mercenaria mercenaria and Southern Quahog Mercenaria campechiensis in Response to Chronic Heat Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:276-292. [PMID: 35357634 DOI: 10.1007/s10126-022-10101-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
The northern quahog (Mercenaria mercenaria) supports lucrative aquaculture industries in the USA. In the southeastern USA, aquacultured M. mercenaria faces increasing risks of summer die-offs from prolonged heat waves. We used a comparative transcriptomic approach to investigate the molecular responses of M. mercenaria and its southern congener, Mercenaria campechiensis, to controlled incremental heat stress over a 4-week period. Mercenaria were exposed to temperatures from 24 to 34 °C with 2.5 °C/week, after which, gill transcriptomes were de novo assembled and annotated. During the 4 weeks of chronic heat exposure, both species had the same survival rate (96%); M. mercenaria experienced body weight gain/loss depending on the originated hatcheries while M. campechiensis experienced an average net weight loss. The upregulated genes in both species included those in chaperone-mediated protein folding and regulation of cell death pathways, while the downregulated genes in both species involved in mRNA processing and splicing pathways. Compared to M. mercenaria, M. campechiensis appears to be more sensitive to prolonged heat stress as indicated by upregulating significantly more genes in coping with oxidative stress and in the protein degradation pathways, while downregulating some inhibitors of apoptosis. We discussed this finding within their ecological and evolutionary context. Our findings highlighted the potential vulnerability of the two quahogs, especially the southern quahog, to continued ocean warming.
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Affiliation(s)
- Jingwei Song
- School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, 7922 NW 71st Street, Gainesville, FL, 32653, USA
| | - James D Austin
- School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, 7922 NW 71st Street, Gainesville, FL, 32653, USA
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, 110 Newins Ziegler Hall, Gainesville, FL, 32611, USA
| | - Huiping Yang
- School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, 7922 NW 71st Street, Gainesville, FL, 32653, USA.
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Srivastava AK, Srivastava R, Bharati AP, Singh AK, Sharma A, Das S, Tiwari PK, Srivastava AK, Chakdar H, Kashyap PL, Saxena AK. Analysis of Biosynthetic Gene Clusters, Secretory, and Antimicrobial Peptides Reveals Environmental Suitability of Exiguobacterium profundum PHM11. Front Microbiol 2022; 12:785458. [PMID: 35185816 PMCID: PMC8851196 DOI: 10.3389/fmicb.2021.785458] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Halotolerant bacteria produce a wide range of bioactive compounds with important applications in agriculture for abiotic stress amelioration and plant growth promotion. In the present study, 17 biosynthetic gene clusters (BGCs) were identified in Exiguobacterium profundum PHM11 belonging to saccharides, desmotamide, pseudaminic acid, dipeptide aldehydes, and terpene biosynthetic pathways representing approximately one-sixth of genomes. The terpene biosynthetic pathway was conserved in Exiguobacterium spp. while the E. profundum PHM11 genome confirms the presence of the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway for the isopentenyl diphosphate (IPP) synthesis. Further, 2,877 signal peptides (SPs) were identified using the PrediSi server, out of which 592 proteins were prophesied for the secretion having a transmembrane helix (TMH). In addition, antimicrobial peptides (AMPs) were also identified using BAGEL4. The transcriptome analysis of PHM11 under salt stress reveals the differential expression of putative secretion and transporter genes having SPs and TMH. Priming of the rice, wheat and maize seeds with PHM11 under salt stress led to improvement in the root length, root diameters, surface area, number of links and forks, and shoot length. The study shows that the presence of BGCs, SPs, and secretion proteins constituting TMH and AMPs provides superior competitiveness in the environment and make E. profundum PHM11 a suitable candidate for plant growth promotion under salt stress.
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Affiliation(s)
- Alok Kumar Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
- Alok Kumar Srivastava,
| | - Ruchi Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Akhilendra Pratap Bharati
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Alok Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Anjney Sharma
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Sudipta Das
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Praveen Kumar Tiwari
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Anchal Kumar Srivastava
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Hillol Chakdar
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Prem Lal Kashyap
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Prem Lal Kashyap, ;
| | - Anil Kumar Saxena
- Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
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Shin TH, Kim SG, Ji M, Kwon DH, Hwang JS, George NP, Ergando DS, Park CB, Paik MJ, Lee G. Diesel-derived PM 2.5 induces impairment of cardiac movement followed by mitochondria dysfunction in cardiomyocytes. Front Endocrinol (Lausanne) 2022; 13:999475. [PMID: 36246901 PMCID: PMC9554599 DOI: 10.3389/fendo.2022.999475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Particulate matter (PM) in polluted air can be exposed to the human body through inhalation, ingestion, and skin contact, accumulating in various organs throughout the body. Organ accumulation of PM is a growing health concern, particularly in the cardiovascular system. PM emissions are formed in the air by solid particles, liquid droplets, and fuel - particularly diesel - combustion. PM2.5 (size < 2.5 μm particle) is a major risk factor for approximately 200,000 premature deaths annually caused by air pollution. This study assessed the deleterious effects of diesel-derived PM2.5 exposure in HL-1 mouse cardiomyocyte cell lines. The PM2.5-induced biological changes, including ultrastructure, intracellular reactive oxygen species (ROS) generation, viability, and intracellular ATP levels, were analyzed. Moreover, we analyzed changes in transcriptomics using RNA sequencing and metabolomics using gas chromatography-tandem mass spectrometry (GC-MS/MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) in PM2.5-treated HL-1 cells. Ultrastructural analysis using transmission electron microscopy revealed disruption of mitochondrial cristae structures in a PM2.5 dose-dependent manner. The elevation of ROS levels and reduction in cell viability and ATP levels were similarly observed in a PM2.5 dose-dependently. In addition, 6,005 genes were differentially expressed (fold change cut-off ± 4) from a total of 45,777 identified genes, and 20 amino acids (AAs) were differentially expressed (fold change cut-off ± 1.2) from a total of 28 identified AAs profiles. Using bioinformatic analysis with ingenuity pathway analysis (IPA) software, we found that the changes in the transcriptome and metabolome are highly related to changes in biological functions, including homeostasis of Ca2+, depolarization of mitochondria, the function of mitochondria, synthesis of ATP, and cardiomyopathy. Moreover, an integrated single omics network was constructed by combining the transcriptome and the metabolome. In silico prediction analysis with IPA predicted that upregulation of mitochondria depolarization, ROS generation, cardiomyopathy, suppression of Ca2+ homeostasis, mitochondrial function, and ATP synthesis occurred in PM2.5-treated HL-1 cells. In particular, the cardiac movement of HL-1 was significantly reduced after PM2.5 treatment. In conclusion, our results assessed the harmful effects of PM2.5 on mitochondrial function and analyzed the biological changes related to cardiac movement, which is potentially associated with cardiovascular diseases.
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Affiliation(s)
- Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Seok Gi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Moongi Ji
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
| | - Do Hyeon Kwon
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Ji Su Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | - Dube Solomon Ergando
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Chan Bae Park
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Man Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- *Correspondence: Man Jeong Paik, ; Gwang Lee,
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- *Correspondence: Man Jeong Paik, ; Gwang Lee,
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Gu X, Chen W, Perry T, Batterham P, Hoffmann AA. Genomic knockout of hsp23 both decreases and increases fitness under opposing thermal extremes in Drosophila melanogaster. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103652. [PMID: 34562590 DOI: 10.1016/j.ibmb.2021.103652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/10/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Under exposure to harmful environmental stresses, organisms exhibit a general stress response involving upregulation of the expression of heat shock proteins (HSPs) which is thought to be adaptive. Small heat shock proteins (sHSPs) are key components of this response, although shsp genes may have other essential roles in development. However, the upregulation of expression of a suite of genes under stress may not necessarily be evidence of an adaptive response to stress that involves those genes. To explore this issue, we used the CRISPR/Cas9 system to investigate pleiotropic effects of the hsp23 gene in Drosophila melanogaster. Transgenic flies carrying a pCFD5 plasmid containing sgRNAs were created to generate a complete knockout of the hsp23 gene. The transgenic line lacking hsp23 showed an increased hatch rate and no major fitness costs under an intermediate temperature used for culturing the flies. In addition, hsp23 knockout affected tolerance to hot and cold temperature extremes but in opposing directions; knockout flies had reduced tolerance to cold, but increased tolerance to heat. Despite this, hsp23 expression (in wild type flies) was increased under both hot and cold conditions. The hsp23 gene was required for heat hardening at the pupal stage, but not at the 1st-instar larval stage, even though the gene was upregulated in wild type controls at that life stage. The phenotypic effects of hsp23 were not compensated for by expression changes in other shsps. Our study shows that the fitness consequences of an hsp gene knockout depends on environmental conditions, with potential fitness benefits of gene loss even under conditions when the gene is normally upregulated.
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Affiliation(s)
- Xinyue Gu
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia.
| | - Wei Chen
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Trent Perry
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Philip Batterham
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
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30
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Shin TH, Manavalan B, Lee DY, Basith S, Seo C, Paik MJ, Kim SW, Seo H, Lee JY, Kim JY, Kim AY, Chung JM, Baik EJ, Kang SH, Choi DK, Kang Y, Maral Mouradian M, Lee G. Silica-coated magnetic-nanoparticle-induced cytotoxicity is reduced in microglia by glutathione and citrate identified using integrated omics. Part Fibre Toxicol 2021; 18:42. [PMID: 34819099 PMCID: PMC8614058 DOI: 10.1186/s12989-021-00433-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Nanoparticles have been utilized in brain research and therapeutics, including imaging, diagnosis, and drug delivery, owing to their versatile properties compared to bulk materials. However, exposure to nanoparticles leads to their accumulation in the brain, but drug development to counteract this nanotoxicity remains challenging. To date, concerns have risen about the potential toxicity to the brain associated with nanoparticles exposure via penetration of the brain blood barrier to address this issue. METHODS Here the effect of silica-coated-magnetic nanoparticles containing the rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)] were assessed on microglia through toxicological investigation, including biological analysis and integration of transcriptomics, proteomics, and metabolomics. MNPs@SiO2(RITC)-induced biological changes, such as morphology, generation of reactive oxygen species, intracellular accumulation of MNPs@SiO2(RITC) using transmission electron microscopy, and glucose uptake efficiency, were analyzed in BV2 murine microglial cells. Each omics data was collected via RNA-sequencing-based transcriptome analysis, liquid chromatography-tandem mass spectrometry-based proteome analysis, and gas chromatography- tandem mass spectrometry-based metabolome analysis. The three omics datasets were integrated and generated as a single network using a machine learning algorithm. Nineteen compounds were screened and predicted their effects on nanotoxicity within the triple-omics network. RESULTS Intracellular reactive oxygen species production, an inflammatory response, and morphological activation of cells were greater, but glucose uptake was lower in MNPs@SiO2(RITC)-treated BV2 microglia and primary rat microglia in a dose-dependent manner. Expression of 121 genes (from 41,214 identified genes), and levels of 45 proteins (from 5918 identified proteins) and 17 metabolites (from 47 identified metabolites) related to the above phenomena changed in MNPs@SiO2(RITC)-treated microglia. A combination of glutathione and citrate attenuated nanotoxicity induced by MNPs@SiO2(RITC) and ten other nanoparticles in vitro and in the murine brain, protecting mostly the hippocampus and thalamus. CONCLUSIONS Combination of glutathione and citrate can be one of the candidates for nanotoxicity alleviating drug against MNPs@SiO2(RITC) induced detrimental effect, including elevation of intracellular reactive oxygen species level, activation of microglia, and reduction in glucose uptake efficiency. In addition, our findings indicate that an integrated triple omics approach provides useful and sensitive toxicological assessment for nanoparticles and screening of drug for nanotoxicity.
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Affiliation(s)
- Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Balachandran Manavalan
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Da Yeon Lee
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Chan Seo
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Suncheon, 57922 Republic of Korea
| | - Man Jeong Paik
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Suncheon, 57922 Republic of Korea
| | - Sang-Wook Kim
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Haewoon Seo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Ju Yeon Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanji-ro, Cheongju, 28119 Republic of Korea
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanji-ro, Cheongju, 28119 Republic of Korea
| | - A Young Kim
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Jee Min Chung
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Eun Joo Baik
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104 Republic of Korea
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104 Republic of Korea
| | - Dong-Kug Choi
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, 268 Chungwondaero, Chungju, 27478 Republic of Korea
| | - Yup Kang
- Department of Physiology, Ajou University School of Medicine, 206 World cup-ro, Suwon, 16499 Republic of Korea
| | - M. Maral Mouradian
- RWJMS Institute for Neurological Therapeutics, Rutgers Biomedical and Health Sciences, and Department of Neurology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854 USA
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon-si, Gyeonggi-do 16499 Republic of Korea
- Department of Physiology, Ajou University School of Medicine, Suwon-si, Gyeonggi-do 16499 Republic of Korea
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Ebner JN. Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. Genes (Basel) 2021; 12:1481. [PMID: 34680873 PMCID: PMC8535992 DOI: 10.3390/genes12101481] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Our ability to predict and assess how environmental changes such as pollution and climate change affect components of the Earth's biome is of paramount importance. This need positioned the fields of ecotoxicology and stress ecology at the center of environmental monitoring efforts. Advances in these interdisciplinary fields depend not only on conceptual leaps but also on technological advances and data integration. High-throughput "omics" technologies enabled the measurement of molecular changes at virtually all levels of an organism's biological organization and thus continue to influence how the impacts of stressors are understood. This bibliometric review describes literature trends (2000-2020) that indicate that more different stressors than species are studied each year but that only a few stressors have been studied in more than two phyla. At the same time, the molecular responses of a diverse set of non-model species have been investigated, but cross-species comparisons are still rare. While transcriptomics studies dominated until 2016, a shift towards proteomics and multiomics studies is apparent. There is now a wealth of data at functional omics levels from many phylogenetically diverse species. This review, therefore, addresses the question of how to integrate omics information across species.
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Affiliation(s)
- Joshua Niklas Ebner
- Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
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Cascarano MC, Stavrakidis-Zachou O, Mladineo I, Thompson KD, Papandroulakis N, Katharios P. Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species. Pathogens 2021; 10:1205. [PMID: 34578236 PMCID: PMC8466566 DOI: 10.3390/pathogens10091205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea.
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Affiliation(s)
- Maria Chiara Cascarano
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Orestis Stavrakidis-Zachou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Ivona Mladineo
- Biology Center of Czech Academy of Sciences, Laboratory of Functional Helminthology, Institute of Parasitology, 370 05 Ceske Budejovice, Czech Republic;
| | - Kim D. Thompson
- Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK;
| | - Nikos Papandroulakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
| | - Pantelis Katharios
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
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Analysis of Nanotoxicity with Integrated Omics and Mechanobiology. NANOMATERIALS 2021; 11:nano11092385. [PMID: 34578701 PMCID: PMC8470953 DOI: 10.3390/nano11092385] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022]
Abstract
Nanoparticles (NPs) in biomedical applications have benefits owing to their small size. However, their intricate and sensitive nature makes an evaluation of the adverse effects of NPs on health necessary and challenging. Since there are limitations to conventional toxicological methods and omics analyses provide a more comprehensive molecular profiling of multifactorial biological systems, omics approaches are necessary to evaluate nanotoxicity. Compared to a single omics layer, integrated omics across multiple omics layers provides more sensitive and comprehensive details on NP-induced toxicity based on network integration analysis. As multi-omics data are heterogeneous and massive, computational methods such as machine learning (ML) have been applied for investigating correlation among each omics. This integration of omics and ML approaches will be helpful for analyzing nanotoxicity. To that end, mechanobiology has been applied for evaluating the biophysical changes in NPs by measuring the traction force and rigidity sensing in NP-treated cells using a sub-elastomeric pillar. Therefore, integrated omics approaches are suitable for elucidating mechanobiological effects exerted by NPs. These technologies will be valuable for expanding the safety evaluations of NPs. Here, we review the integration of omics, ML, and mechanobiology for evaluating nanotoxicity.
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34
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Eskew EA, Fraser D, Vonhof MJ, Pinsky ML, Maslo B. Host gene expression in wildlife disease: making sense of species-level responses. Mol Ecol 2021; 30:6517-6530. [PMID: 34516689 DOI: 10.1111/mec.16172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species-specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease-resistant and disease-susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease-resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease-resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these "null" findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species-specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation-relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.
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Affiliation(s)
- Evan A Eskew
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.,Department of Biology, Pacific Lutheran University, Tacoma, Washington, USA
| | - Devaughn Fraser
- Wildlife Genetics Research Laboratory, California Department of Fish and Wildlife, Sacramento, California, USA
| | - Maarten J Vonhof
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Malin L Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Brooke Maslo
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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35
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Mackey TE, Hasler CT, Durhack T, Jeffrey JD, Macnaughton CJ, Ta K, Enders EC, Jeffries KM. Molecular and physiological responses predict acclimation limits in juvenile brook trout (Salvelinus fontinalis). J Exp Biol 2021; 224:271813. [PMID: 34382658 DOI: 10.1242/jeb.241885] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/13/2021] [Indexed: 11/20/2022]
Abstract
Understanding the resilience of ectotherms to high temperatures is essential because of the influence of climate change on aquatic ecosystems. The ability of species to acclimate to high temperatures may determine whether populations can persist in their native ranges. We examined physiological and molecular responses of juvenile brook trout (Salvelinus fontinalis) to six acclimation temperatures (5, 10, 15, 20, 23 and 25°C) that span the thermal distribution of the species to predict acclimation limits. Brook trout exhibited an upregulation of stress-related mRNA transcripts (heat shock protein 90-beta, heat shock cognate 71 kDa protein, glutathione peroxidase 1) and downregulation of transcription factors and osmoregulation-related transcripts (nuclear protein 1, Na+/K+/2Cl- co-transporter-1-a) at temperatures ≥20°C. We then examined the effects of acclimation temperature on metabolic rate (MR) and physiological parameters in fish exposed to an acute exhaustive exercise and air exposure stress. Fish acclimated to temperatures ≥20°C exhibited elevated plasma cortisol and glucose, and muscle lactate after exposure to the acute stress. Fish exhibited longer MR recovery times at 15 and 20°C compared with the 5 and 10°C groups; however, cortisol levels remained elevated at temperatures ≥20°C after 24 h. Oxygen consumption in fish acclimated to 23°C recovered quickest after exposure to acute stress. Standard MR was highest and factorial aerobic scope was lowest for fish held at temperatures ≥20°C. Our findings demonstrate how molecular and physiological responses predict acclimation limits in a freshwater fish as the brook trout in the present study had a limited ability to acclimate to temperatures beyond 20°C.
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Affiliation(s)
- Theresa E Mackey
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada, R3B 2E9
| | - Caleb T Hasler
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada, R3B 2E9
| | - Travis Durhack
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2.,Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, MB, Canada, R3T 2N6
| | - Jennifer D Jeffrey
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | | | - Kimberly Ta
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | - Eva C Enders
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, MB, Canada, R3T 2N6
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
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36
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Root L, Campo A, MacNiven L, Con P, Cnaani A, Kültz D. Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover. Genomics 2021; 113:3235-3249. [PMID: 34298068 DOI: 10.1016/j.ygeno.2021.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/25/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022]
Abstract
A data-independent acquisition (DIA) assay library for targeted quantitation of thousands of Oreochromis niloticus gill proteins using a label- and gel-free workflow was generated and used to compare protein and mRNA abundances. This approach generated complimentary rather than redundant data for 1899 unique genes in gills of tilapia acclimated to freshwater and brackish water. Functional enrichment analyses identified mitochondrial energy metabolism, serine protease and immunity-related functions, and cytoskeleton/ extracellular matrix organization as major processes controlled by salinity in O. niloticus gills. Non-linearity in salinity-dependent transcriptome versus proteome regulation was revealed for specific functional groups of genes. The relationship was more linear for other molecular functions/ cellular processes, suggesting that the salinity-dependent regulation of O. niloticus gill function relies on post-transcriptional mechanisms for some functions/ processes more than others. This integrative systems biology approach can be adopted for other tissues and organisms to study cellular dynamics for many changing ecological contexts.
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Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Aurora Campo
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Leah MacNiven
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA.
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37
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Lopez-Anido RN, Harrington AM, Hamlin HJ. Coping with stress in a warming Gulf: the postlarval American lobster's cellular stress response under future warming scenarios. Cell Stress Chaperones 2021; 26:721-734. [PMID: 34115338 PMCID: PMC8275755 DOI: 10.1007/s12192-021-01217-1] [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: 02/15/2021] [Revised: 05/18/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022] Open
Abstract
The Gulf of the Maine (GoM) is one of the fastest warming bodies of water in the world, posing serious physiological challenges to its marine inhabitants. Marine organisms can cope with the cellular and molecular stresses created by climate change through changes in gene expression. We used transcriptomics to examine how exposure to current summer temperatures (16 °C) or temperature regimes reflective of projected moderate and severe warming conditions (18 °C and 22 °C, respectively) during larval development alters expression of transcripts affiliated with the cellular stress response (CSR) in postlarval American lobsters (Homarus americanus). We identified 26 significantly differentially expressed (DE) transcripts annotated to CSR proteins. Specifically, transcripts for proteins affiliated with heat shock, the ubiquitin family, DNA repair, and apoptosis were significantly over-expressed in lobsters reared at higher temperatures relative to current conditions. Substantial variation in the CSR expression between postlarvae reared at 18 °C and those reared at 22 °C suggests that postlarvae reared under severe warming may have a hindered ability to cope with the physiological and molecular challenges of ocean warming. These results highlight that postlarval American lobsters may experience significant heat stress as rapid warming in the GoM continues, potentially compromising their ability to prevent cellular damage and inhibiting the reallocation of cellular energy towards other physiological functions beyond activation of the CSR. Moreover, this study establishes additional American lobster stress markers and addresses various knowledge gaps in crustacean biology, where sufficient 'omics research is lacking.
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Affiliation(s)
| | - Amalia M Harrington
- Maine Sea Grant College Program, University of Maine, 5741 Libby Hall, Room 121, Orono, ME, 04469, USA.
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA.
| | - Heather J Hamlin
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
- Aquaculture Research Institute, University of Maine, Orono, ME, 04469, USA
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38
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Root L, Campo A, MacNiven L, Con P, Cnaani A, Kültz D. A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus. Mol Ecol Resour 2021; 21:2486-2503. [PMID: 34101993 DOI: 10.1111/1755-0998.13445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 12/31/2022]
Abstract
Interactions of organisms with their environment are complex and environmental regulation at different levels of biological organization is often nonlinear. Therefore, the genotype to phenotype continuum requires study at multiple levels of organization. While studies of transcriptome regulation are now common for many species, quantitative studies of environmental effects on proteomes are needed. Here we report the generation of a data-independent acquisition (DIA) assay library that enables simultaneous targeted proteomics of thousands of Oreochromis niloticus kidney proteins using a label- and gel-free workflow that is well suited for ecologically relevant field samples. We demonstrate the usefulness of this DIA assay library by discerning environmental effects on the kidney proteome of O. niloticus. Moreover, we demonstrate that the DIA assay library approach generates data that are complimentary rather than redundant to transcriptomic data. Transcript and protein abundance differences in kidneys of tilapia acclimated to freshwater and brackish water (25 g/kg) were correlated for 2114 unique genes. A high degree of non-linearity in salinity-dependent regulation of transcriptomes and proteomes was revealed suggesting that the regulation of O. niloticus renal function by environmental salinity relies heavily on post-transcriptional mechanisms. The application of functional enrichment analyses using STRING and KEGG to DIA assay data sets is demonstrated by identifying myo-inositol metabolism, antioxidant and xenobiotic functions, and signalling mechanisms as key elements controlled by salinity in tilapia kidneys. The DIA assay library resource presented here can be adopted for other tissues and other organisms to study proteome dynamics during changing ecological contexts.
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Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| | - Aurora Campo
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Leah MacNiven
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| | - Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
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Chakraborty S, Gourain V, Benz M, Scheiger J, Levkin P, Popova A. Droplet microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape. Mater Today Bio 2021; 11:100112. [PMID: 34124640 PMCID: PMC8175407 DOI: 10.1016/j.mtbio.2021.100112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
The development of novel chemically developed and physically defined surfaces and environments for cell culture and screening is important for various biological applications. The Droplet microarray (DMA) platform based on hydrophilic-superhydrophobic patterning enables high-throughput cellular screening in nanoliter volumes and on various biocompatible surfaces. Here we performed phenotypic and transcriptomic analysis of HeLa-CCL2 cells cultured on DMA, with a goal to analyze cellular response on different surfaces and culture volumes down to 3 nL, compared with conventional cell culture platforms. Our results indicate that cells cultured on four tested substrates: nanostructured nonpolymer, rough and smooth variants of poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) polymer and poly(thioether) dendrimer are compatible with cells grown in Petri dish. Cells cultured on nanostructured nonpolymer coating exhibited the closet transcriptomic resemblance to that of cells grown in Petri dish. Analysis of cells cultured in 100, 9, and 3 nL media droplets on DMA indicated that all but cells grown in 3 nL volumes had unperturbed viability with minimal alterations in the transcriptome compared with 96-well plate. Our findings demonstrate the applicability of DMA for cell-based assays and highlight the possibility of establishing regular cell culture on various biomaterial-coated substrates and in nanoliter volumes, along with routinely used cell culture platforms.
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Affiliation(s)
- S. Chakraborty
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| | - V. Gourain
- Institute of Biological and Chemical Systems–Biological Information Processing (IBCS–BIP), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| | - M. Benz
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| | - J.M. Scheiger
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
- Institute of Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstr. 20, 76131 Karlsruhe, Germany
| | - P.A. Levkin
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 6, 76131 Karlsruhe, Germany
| | - A.A. Popova
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
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40
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The influence of hypoxia on the cardiac transcriptomes of two estuarine species - C. variegatus and F. grandis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100837. [PMID: 33892309 DOI: 10.1016/j.cbd.2021.100837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/21/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023]
Abstract
Increased nutrient loading has led to eutrophication of coastal shelf waters which has resulted in increased prevalence of persistent hypoxic zones - areas in which the dissolved oxygen content of the water drops below 2 mg/L. The northern Gulf of Mexico, fed primarily by the Mississippi River watershed, undergoes annual establishment of one of the largest hypoxic zones in the world. Exposure to hypoxia can induce physiological impacts in fish cardiac systems that include bradycardia, changes in stroke volume, and altered cardiovascular vessel development. While these impacts have been addressed at the functional level, there is little information regarding the molecular basis for these changes. This study used transcriptomic analysis techniques to interrogate the effects of hypoxia exposure on the developing cardiovascular system in newly hatched larvae of two estuarine species that occupy the same ecological niche - the sheepshead minnow (Cyprinodon variegatus) and the Gulf killifish (Fundulus grandis). Results suggest that while differential gene expression is largely distinct between the two species, downstream impacts on pathways and functional responses such as reduced cardiac hypertrophy, modulation of blood pressure, and increased incidence of apoptosis appear to be conserved. Further, differences in the magnitude of these conserved responses may suggest that the length of embryonic development could impart a level of resiliency to hypoxic perturbation in early life stage fish.
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41
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Rocha JL, Godinho R, Brito JC, Nielsen R. Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation. Trends Ecol Evol 2021; 36:637-650. [PMID: 33863602 DOI: 10.1016/j.tree.2021.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different desert mammals show large overlap in functional classes of genes and pathways, consistent with the complexity and variety of phenotypes associated with desert adaptation to water and food scarcity and extreme temperatures. However, studies of desert adaptation are also challenged by a lack of accurate genotype-phenotype-environment maps. We encourage development of systems that facilitate functional analyses, but also acknowledge the need for more studies on a wider variety of desert mammals.
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Affiliation(s)
- Joana L Rocha
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Department of Zoology, University of Johannesburg, PO Box 534, Auckland Park 2006, South Africa
| | - José C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA 94820, USA; Globe Institute, University of Copenhagen, DK-1165 Copenhagen, Denmark.
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42
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Plagens RN, Mossiah I, Kim Guisbert KS, Guisbert E. Chronic temperature stress inhibits reproduction and disrupts endocytosis via chaperone titration in Caenorhabditis elegans. BMC Biol 2021; 19:75. [PMID: 33858388 PMCID: PMC8051109 DOI: 10.1186/s12915-021-01008-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background Temperature influences biology at all levels, from altering rates of biochemical reactions to determining sustainability of entire ecosystems. Although extended exposure to elevated temperatures influences organismal phenotypes important for human health, agriculture, and ecology, the molecular mechanisms that drive these responses remain largely unexplored. Prolonged, mild temperature stress (48 h at 28 °C) has been shown to inhibit reproduction in Caenorhabditis elegans without significantly impacting motility or viability. Results Analysis of molecular responses to chronic stress using RNA-seq uncovers dramatic effects on the transcriptome that are fundamentally distinct from the well-characterized, acute heat shock response (HSR). While a large portion of the genome is differentially expressed ≥ 4-fold after 48 h at 28 °C, the only major class of oogenesis-associated genes affected is the vitellogenin gene family that encodes for yolk proteins (YPs). Whereas YP mRNAs decrease, the proteins accumulate and mislocalize in the pseudocoelomic space as early as 6 h, well before reproduction declines. A trafficking defect in a second, unrelated fluorescent reporter and a decrease in pre-synaptic neuronal signaling indicate that the YP mislocalization is caused by a generalized defect in endocytosis. Molecular chaperones are involved in both endocytosis and refolding damaged proteins. Decreasing levels of the major HSP70 chaperone, HSP-1, causes similar YP trafficking defects in the absence of stress. Conversely, increasing chaperone levels through overexpression of the transcription factor HSF-1 rescues YP trafficking and restores neuronal signaling. Conclusions These data implicate chaperone titration during chronic stress as a molecular mechanism contributing to endocytic defects that influence multiple aspects of organismal physiology. Notably, HSF-1 overexpression improves recovery of viable offspring after exposure to stress. These findings provide important molecular insights into understanding organismal responses to temperature stress as well as phenotypes associated with chronic protein misfolding. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01008-1.
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Affiliation(s)
- Rosemary N Plagens
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Isiah Mossiah
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Karen S Kim Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Eric Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA.
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Sokolova I. Bioenergetics in environmental adaptation and stress tolerance of aquatic ectotherms: linking physiology and ecology in a multi-stressor landscape. J Exp Biol 2021; 224:224/Suppl_1/jeb236802. [PMID: 33627464 DOI: 10.1242/jeb.236802] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Energy metabolism (encompassing energy assimilation, conversion and utilization) plays a central role in all life processes and serves as a link between the organismal physiology, behavior and ecology. Metabolic rates define the physiological and life-history performance of an organism, have direct implications for Darwinian fitness, and affect ecologically relevant traits such as the trophic relationships, productivity and ecosystem engineering functions. Natural environmental variability and anthropogenic changes expose aquatic ectotherms to multiple stressors that can strongly affect their energy metabolism and thereby modify the energy fluxes within an organism and in the ecosystem. This Review focuses on the role of bioenergetic disturbances and metabolic adjustments in responses to multiple stressors (especially the general cellular stress response), provides examples of the effects of multiple stressors on energy intake, assimilation, conversion and expenditure, and discusses the conceptual and quantitative approaches to identify and mechanistically explain the energy trade-offs in multiple stressor scenarios, and link the cellular and organismal bioenergetics with fitness, productivity and/or ecological functions of aquatic ectotherms.
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Affiliation(s)
- Inna Sokolova
- Marine Biology Department, Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany .,Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
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Schoville SD, Simon S, Bai M, Beethem Z, Dudko RY, Eberhard MJB, Frandsen PB, Küpper SC, Machida R, Verheij M, Willadsen PC, Zhou X, Wipfler B. Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. Evol Appl 2021; 14:360-382. [PMID: 33664782 PMCID: PMC7896716 DOI: 10.1111/eva.13120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/25/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022] Open
Abstract
Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.
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Affiliation(s)
| | - Sabrina Simon
- Biosystematics GroupWageningen University & ResearchPB WageningenThe Netherlands
| | - Ming Bai
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zachary Beethem
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Department of Biomedical SciencesSchool of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Roman Y. Dudko
- Institute of Systematics and Ecology of AnimalsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
- Tomsk State UniversityTomskRussia
| | - Monika J. B. Eberhard
- Zoological Institute and MuseumGeneral Zoology and Zoological SystematicsUniversity of GreifswaldGreifswaldGermany
| | - Paul B. Frandsen
- Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUTUSA
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonDCU.S.A
| | - Simon C. Küpper
- Zoological Institute and MuseumGeneral Zoology and Zoological SystematicsUniversity of GreifswaldGreifswaldGermany
| | - Ryuichiro Machida
- Sugadaira Research StationMountain Science CenterUniversity of TsukubaUeda, NaganoJapan
| | - Max Verheij
- Biosystematics GroupWageningen University & ResearchPB WageningenThe Netherlands
| | - Peter C. Willadsen
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityCampus Box 7613RaleighNCUSA
| | - Xin Zhou
- Department of EntomologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
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Shin TH, Ketebo AA, Lee DY, Lee S, Kang SH, Basith S, Manavalan B, Kwon DH, Park S, Lee G. Decrease in membrane fluidity and traction force induced by silica-coated magnetic nanoparticles. J Nanobiotechnology 2021; 19:21. [PMID: 33430909 PMCID: PMC7802323 DOI: 10.1186/s12951-020-00765-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background Nanoparticles are being increasingly used in biomedical applications owing to their unique physical and chemical properties and small size. However, their biophysical assessment and evaluation of side-effects remain challenging. We addressed this issue by investigating the effects of silica-coated magnetic nanoparticles containing rhodamine B isothiocyanate [MNPs@SiO2(RITC)] on biophysical aspects, such as membrane fluidity and traction force of human embryonic kidney 293 (HEK293) cells. We further extended our understanding on the biophysical effects of nanoparticles on cells using a combination of metabolic profiling and transcriptomic network analysis. Results Overdose (1.0 μg/µL) treatment with MNPs@SiO2(RITC) induced lipid peroxidation and decreased membrane fluidity in HEK293 cells. In addition, HEK293 cells were morphologically shrunk, and their aspect ratio was significantly decreased. We found that each traction force (measured in micropillar) was increased, thereby increasing the total traction force in MNPs@SiO2(RITC)-treated HEK293 cells. Due to the reduction in membrane fluidity and elevation of traction force, the velocity of cell movement was also significantly decreased. Moreover, intracellular level of adenosine triphosphate (ATP) was also decreased in a dose-dependent manner upon treatment with MNPs@SiO2(RITC). To understand these biophysical changes in cells, we analysed the transcriptome and metabolic profiles and generated a metabotranscriptomics network, which revealed relationships among peroxidation of lipids, focal adhesion, cell movement, and related genes and metabolites. Furthermore, in silico prediction of the network showed increment in the peroxidation of lipids and suppression of focal adhesion and cell movement. Conclusion Taken together, our results demonstrated that overdose of MNPs@SiO2(RITC) impairs cellular movement, followed by changes in the biophysical properties of cells, thus highlighting the need for biophysical assessment of nanoparticle-induced side-effects. ![]()
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Affiliation(s)
- Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Abdurazak Aman Ketebo
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Da Yeon Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, 17104, Republic of Korea
| | - Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Balachandran Manavalan
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Do Hyeon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea. .,Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
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Komoroske LM, Jeffries KM, Whitehead A, Roach JL, Britton M, Connon RE, Verhille C, Brander SM, Fangue NA. Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish. Evol Appl 2020. [DOI: 10.1111/eva.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
| | - Ken M. Jeffries
- Department of Biological Sciences University of Manitoba Winnipeg MB Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Jennifer L. Roach
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center University of California, Davis Davis CA USA
| | - Richard E. Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine University of California, Davis Davis CA USA
| | | | - Susanne M. Brander
- Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station Oregon State University Corvallis OR USA
| | - Nann A. Fangue
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
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47
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Wang Q, Hao X, Liu K, Feng B, Li S, Zhang Z, Tang L, Mahboob S, Shao C. Early response to heat stress in Chinese tongue sole (Cynoglossus semilaevis): performance of different sexes, candidate genes and networks. BMC Genomics 2020; 21:745. [PMID: 33109079 PMCID: PMC7590793 DOI: 10.1186/s12864-020-07157-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Temperature is known to affect living organisms and alter the expression of responsive genes, which affects a series of life processes, such as development, reproduction and metabolism. Several genes and gene families have been involved in high temperature responses, such as heat shock protein (hsp) family, Jumonji family and genes related to cortisol synthesis. Gonad is a vital organ related to the existence of a species. However, the comprehensive understanding of gonadal responses to environmental temperature is limited. RESULTS To explore the effects of environmental temperature on genes and gene networks in gonads, we performed acute heat treatment (48 h) on Chinese tongue sole (Cynoglossus semilaevis). Gonadal transcriptome analysis was conducted on females, pseudomales and males exposed to high (28 °C) and normal (22 °C) temperatures. A total of 1226.24 million clean reads were obtained from 18 libraries. Principal component analysis (PCA) and differentially expressed gene (DEG) analysis revealed different performance of sex responses to heat stress. There were 4565, 790 and 1117 specific genes altered their expression level in females, pseudomales and males, respectively. Of these, genes related to hsp gene family, cortisol synthesis and metabolism and epigenetic regulation were involved in early heat response. Furthermore, a total of 1048 DEGs were shared among females, pesudomales and males, which may represent the inherent difference between high and normal temperatures. Genes, such as eef1akmt3, eef1akmt4, pnmt and hsp family members, were found. CONCLUSIONS Our results depicted for the first time the gonadal gene expression under acute high temperature treatment in Chinese tongue sole. The findings may provide a clue for understanding the responses of genes and networks to environmental temperature.
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Affiliation(s)
- Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Xiancai Hao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Bo Feng
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Shuo Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Zhihua Zhang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
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48
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Fletcher E, Baetz K. Multi-Faceted Systems Biology Approaches Present a Cellular Landscape of Phenolic Compound Inhibition in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:539902. [PMID: 33154962 PMCID: PMC7591714 DOI: 10.3389/fbioe.2020.539902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023] Open
Abstract
Synthetic biology has played a major role in engineering microbial cell factories to convert plant biomass (lignocellulose) to fuels and bioproducts by fermentation. However, the final product yield is limited by inhibition of microbial growth and fermentation by toxic phenolic compounds generated during lignocellulosic pre-treatment and hydrolysis. Advances in the development of systems biology technologies (genomics, transcriptomics, proteomics, metabolomics) have rapidly resulted in large datasets which are necessary to obtain a holistic understanding of complex biological processes underlying phenolic compound toxicity. Here, we review and compare different systems biology tools that have been utilized to identify molecular mechanisms that modulate phenolic compound toxicity in Saccharomyces cerevisiae. By focusing on and comparing functional genomics and transcriptomics approaches we identify common mechanisms potentially underlying phenolic toxicity. Additionally, we discuss possible ways by which integration of data obtained across multiple unbiased approaches can result in new avenues to develop yeast strains with a significant improvement in tolerance to phenolic fermentation inhibitors.
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Affiliation(s)
- Eugene Fletcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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49
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Biales AD, Bencic DC, Flick RW, Delacruz A, Gordon DA, Huang W. Global transcriptomic profiling of microcystin-LR or -RR treated hepatocytes (HepaRG). Toxicon X 2020; 8:100060. [PMID: 33235993 PMCID: PMC7670210 DOI: 10.1016/j.toxcx.2020.100060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
The canonical mode of action (MOA) of microcystins (MC) is the inhibition of protein phosphatases, but complete characterization of toxicity pathways is lacking. The existence of over 200 MC congeners complicates risk estimates worldwide. This work employed RNA-seq to provide an unbiased and comprehensive characterization of cellular targets and impacted cellular processes of hepatocytes exposed to either MC-LR or MC-RR congeners. The human hepatocyte cell line, HepaRG, was treated with three concentrations of MC-LR or -RR for 2 h. Significant reduction in cell survival was observed in LR1000 and LR100 treatments whereas no acute toxicity was observed in any MR-RR treatment. RNA-seq was performed on all treatments of MC-LR and -RR. Differentially expressed genes and pathways associated with oxidative and endoplasmic reticulum (ER) stress, and the unfolded protein response (UPR) were highly enriched by both congeners as were inflammatory pathways. Genes associated with both apoptotic and inflammatory pathways were enriched in LR1000. We present a model of MC toxicity that immediately causes oxidative stress and leads to ER stress and the activation of the UPR. Differential activation of the three arms of the UPR and the kinetics of JNK activation ultimately determine whether cell survival or apoptosis is favored. Extracellular exosomes were enrichment of by both congeners, suggesting a previously unidentified mechanism for MC-dependent extracellular signaling. The complement system was enriched only in MC-RR treatments, suggesting congener-specific differences in cellular effects. This study provided an unbiased snapshot of the early systemic hepatocyte response to MC-LR and MC-RR congeners and may explain differences in toxicity among MC congeners. Microcystin-LR and microcystin-RR have similar transcriptional responses. Genes associated with oxidative stress and the unfolded protein response were enriched by congeners. Genes associated with extracellular exosomes were enriched, suggesting a potential new mechanism for cell signaling. Complement associated genes were strongly enriched only by microcystin-RR. Identified a potential molecular mechanism underlying the cellular fate of hepatocyte.
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Affiliation(s)
- Adam D Biales
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA
| | - David C Bencic
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA
| | - Robert W Flick
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA
| | - Armah Delacruz
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA
| | - Denise A Gordon
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA
| | - Weichun Huang
- U.S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC, 27709, USA
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50
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Martyniuk CJ. Perspectives on transcriptomics in animal physiology studies. Comp Biochem Physiol B Biochem Mol Biol 2020; 250:110490. [PMID: 32798690 DOI: 10.1016/j.cbpb.2020.110490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/05/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022]
Abstract
Reductionist approaches in physiology and biochemistry are essential for understanding how animals cope and adapt to their environments. Transcriptomics is no longer restricted to a select few, and accessibility and affordability continue to facilitate its rapid growth as a science. More than 6000 publications (a conservative estimate) over the past decade quantify the response of the transcriptome to a wide breadth of questions in animal physiology. Transcriptomes have been quantified under conditions of hypoxia, climate change, salinity, drought, environmental pollution, and ultraviolet radiation among others; these studies have greatly improved understanding of the molecular machinery required for organismal adaptation. These "snapshots in time" however are never complete as the transcriptome is exquisitely sensitive to an individual's current physiologic state. Animal physiologists new to the field must recognize limitations of transcriptome technologies and consider experimental designs that strengthen physiologic interpretation. Current estimates suggest that a sample size of 6 or more are required for RNA-seq experiments in order to capture the majority of differentially expressed genes confidently. "Outside-the-box" approaches for statistical analyses of data derived from RNA-seq should be explored, as studies continue to point out that high false discoveries rates are pervasive with RNA-seq studies, reminiscent of the early days of microarrays. Incorporating biological variability, rather than reducing it (i.e. pooling strategies), into experimental designs is essential. Moreover, real-time PCR must not be viewed as a "validation step" to justify low samples sizes, but rather an orthogonal method to strengthen biological interpretation. The use of proper experimental controls in transcriptomics studies (i.e. spike-in controls and technical replication) are recommended and there is a pressing need for inter-laboratory tests (round robin experiments) to quantify repeatability and to identify sources of transcriptome variation within the context of animal physiology. Testing the reproducibility of transcriptome experiments in light of physiology in non-model organisms would be a significant contribution to the community. Single cell transcriptomics and multiplexing barcoding strategies such as decode-seq are poised to further advance the reductionist view of animal physiology; researchers are encouraged to consult literature herein and elsewhere for guidance on best practices and limitations of transcriptome technologies when studying the physiology of animals.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.
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