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Mansoor S, Tripathi P, Ghimire A, Hamid S, Abd El-Moniem D, Chung YS, Kim Y. Comparative transcriptomic analysis of the nodulation-competent zone and inference of transcription regulatory network in silicon applied Glycine max [L.]-Merr. Roots. PLANT CELL REPORTS 2024; 43:169. [PMID: 38864921 PMCID: PMC11169057 DOI: 10.1007/s00299-024-03250-7] [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: 02/22/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
KEY MESSAGE The study unveils Si's regulatory influence by regulating DEGs, TFs, and TRs. Further bHLH subfamily and auxin transporter pathway elucidates the mechanisms enhancing root development and nodulation. Soybean is a globally important crop serving as a primary source of vegetable protein for millions of individuals. The roots of these plants harbour essential nitrogen fixing structures called nodules. This study investigates the multifaceted impact of silicon (Si) application on soybean, with a focus on root development, and nodulation employing comprehensive transcriptomic analyses and gene regulatory network. RNA sequence analysis was utilised to examine the change in gene expression and identify the noteworthy differentially expressed genes (DEGs) linked to the enhancement of soybean root nodulation and root development. A set of 316 genes involved in diverse biological and molecular pathways are identified, with emphasis on transcription factors (TFs) and transcriptional regulators (TRs). The study uncovers TF and TR genes, categorized into 68 distinct families, highlighting the intricate regulatory landscape influenced by Si in soybeans. Upregulated most important bHLH subfamily and the involvement of the auxin transporter pathway underscore the molecular mechanisms contributing to enhanced root development and nodulation. The study bridges insights from other research, reinforcing Si's impact on stress-response pathways and phenylpropanoid biosynthesis crucial for nodulation. The study reveals significant alterations in gene expression patterns associated with cellular component functions, root development, and nodulation in response to Si.
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Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea
| | - Pooja Tripathi
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, USA
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamia University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Diaa Abd El-Moniem
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea.
| | - Yoonha Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Li H, Khang TF. clrDV: a differential variability test for RNA-Seq data based on the skew-normal distribution. PeerJ 2023; 11:e16126. [PMID: 37790621 PMCID: PMC10544356 DOI: 10.7717/peerj.16126] [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: 02/24/2023] [Accepted: 08/27/2023] [Indexed: 10/05/2023] Open
Abstract
Background Pathological conditions may result in certain genes having expression variance that differs markedly from that of the control. Finding such genes from gene expression data can provide invaluable candidates for therapeutic intervention. Under the dominant paradigm for modeling RNA-Seq gene counts using the negative binomial model, tests of differential variability are challenging to develop, owing to dependence of the variance on the mean. Methods Here, we describe clrDV, a statistical method for detecting genes that show differential variability between two populations. We present the skew-normal distribution for modeling gene-wise null distribution of centered log-ratio transformation of compositional RNA-seq data. Results Simulation results show that clrDV has false discovery rate and probability of Type II error that are on par with or superior to existing methodologies. In addition, its run time is faster than its closest competitors, and remains relatively constant for increasing sample size per group. Analysis of a large neurodegenerative disease RNA-Seq dataset using clrDV successfully recovers multiple gene candidates that have been reported to be associated with Alzheimer's disease.
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Affiliation(s)
- Hongxiang Li
- Institute of Mathematical Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Tsung Fei Khang
- Institute of Mathematical Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Universiti Malaya Centre for Data Analytics, Universiti Malaya, Kuala Lumpur, Malaysia
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Elsamad G, Mecawi AS, Pauža AG, Gillard B, Paterson A, Duque VJ, Šarenac O, Žigon NJ, Greenwood M, Greenwood MP, Murphy D. Ageing restructures the transcriptome of the hypothalamic supraoptic nucleus and alters the response to dehydration. NPJ AGING 2023; 9:12. [PMID: 37264028 PMCID: PMC10234251 DOI: 10.1038/s41514-023-00108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/04/2023] [Indexed: 06/03/2023]
Abstract
Ageing is associated with altered neuroendocrine function. In the context of the hypothalamic supraoptic nucleus, which makes the antidiuretic hormone vasopressin, ageing alters acute responses to hyperosmotic cues, rendering the elderly more susceptible to dehydration. Chronically, vasopressin has been associated with numerous diseases of old age, including type 2 diabetes and metabolic syndrome. Bulk RNAseq transcriptome analysis has been used to catalogue the polyadenylated supraoptic nucleus transcriptomes of adult (3 months) and aged (18 months) rats in basal euhydrated and stimulated dehydrated conditions. Gene ontology and Weighted Correlation Network Analysis revealed that ageing is associated with alterations in the expression of extracellular matrix genes. Interestingly, whilst the transcriptomic response to dehydration is overall blunted in aged animals compared to adults, there is a specific enrichment of differentially expressed genes related to neurodegenerative processes in the aged cohort, suggesting that dehydration itself may provoke degenerative consequences in aged rats.
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Affiliation(s)
- Ghadir Elsamad
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - André Souza Mecawi
- Laboratory of Molecular Neuroendocrinology, Department of Biophysics, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Audrys G Pauža
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
- Translational Cardio-Respiratory Research Group, Department of Physiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Benjamin Gillard
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - Alex Paterson
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
- Insilico Consulting Ltd., Wapping Wharf, Bristol, England
| | - Victor J Duque
- Laboratory of Molecular Neuroendocrinology, Department of Biophysics, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Olivera Šarenac
- Institute of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Department of Safety Pharmacology, Abbvie, North Chicago, Illinois, USA
| | - Nina Japundžić Žigon
- Institute of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Mingkwan Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - Michael P Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, Dorothy Hodgkin Building, University of Bristol, Bristol, England.
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Labory J, Le Bideau G, Pratella D, Yao JE, Ait-El-Mkadem Saadi S, Bannwarth S, El-Hami L, Paquis-Fluckinger V, Bottini S. ABEILLE: a novel method for ABerrant Expression Identification empLoying machine Learning from RNA-sequencing data. Bioinformatics 2022; 38:4754-4761. [PMID: 36063052 PMCID: PMC9563686 DOI: 10.1093/bioinformatics/btac603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Current advances in omics technologies are paving the diagnosis of rare diseases proposing as a complementary assay to identify the responsible gene. The use of transcriptomic data to identify aberrant gene expression (AGE) have demonstrated to yield potential pathogenic events. However popular approaches for AGE identification are limited by the use of statistical tests that imply the choice of arbitrary cut-off for significance assessment and the availability of several replicates not always possible in clinical contexts. RESULTS Hence we developed ABEILLE (ABerrant Expression Identification empLoying machine LEarning from sequencing data) a variational autoencoder (VAE) based method for the identification of AGEs from the analysis of RNA-seq data without the need of replicates or a control group. ABEILLE combines the use of a VAE, able to model any data without specific assumptions on their distribution, and a decision tree to classify genes as AGE or non-AGE. An anomaly score is associated to each gene in order to stratify AGE by severity of aberration. We tested ABEILLE on semi-synthetic and an experimental dataset demonstrating the importance of the flexibility of the VAE configuration to identify potential pathogenic candidates. AVAILABILITY ABEILLE source code is freely available at : https://github.com/UCA-MSI/ABEILLE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justine Labory
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France.,Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Gwendal Le Bideau
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - David Pratella
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Jean-Elisée Yao
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Samira Ait-El-Mkadem Saadi
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Loubna El-Hami
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France.,Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Véronique Paquis-Fluckinger
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Silvia Bottini
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
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Greenwood M, Gillard BT, Farrukh R, Paterson A, Althammer F, Grinevich V, Murphy D, Greenwood MP. Transcription factor Creb3l1 maintains proteostasis in neuroendocrine cells. Mol Metab 2022; 63:101542. [PMID: 35803572 PMCID: PMC9294333 DOI: 10.1016/j.molmet.2022.101542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES Dynamic changes to neuropeptide hormone synthesis and secretion by hypothalamic neuroendocrine cells is essential to ensure metabolic homeostasis. The specialised molecular mechanisms that allow neuroendocrine cells to synthesise and secrete vast quantities of neuropeptides remain ill defined. The objective of this study was to identify novel genes and pathways controlled by transcription factor and endoplasmic reticulum stress sensor Creb3l1 which is robustly activated in hypothalamic magnocellular neurones in response to increased demand for protein synthesis. METHODS We adopted a multiomic strategy to investigate specific roles of Creb3l1 in rat magnocellular neurones. We first performed chromatin immunoprecipitation followed by genome sequencing (ChIP-seq) to identify Creb3l1 genomic targets and then integrated this data with RNA sequencing data from physiologically stimulated and Creb3l1 knockdown magnocellular neurones. RESULTS The data converged on Creb3l1 targets that code for ribosomal proteins and endoplasmic reticulum proteins crucial for the maintenance of cellular proteostasis. We validated genes that compose the PERK arm of the unfolded protein response pathway including Eif2ak3, Eif2s1, Atf4 and Ddit3 as direct Creb3l1 targets. Importantly, knockdown of Creb3l1 in the hypothalamus led to a dramatic depletion in neuropeptide synthesis and secretion. The physiological outcomes from studies of paraventricular and supraoptic nuclei Creb3l1 knockdown animals were changes to food and water consumption. CONCLUSION Collectively, our data identify Creb3l1 as a comprehensive controller of the PERK signalling pathway in magnocellular neurones in response to physiological stimulation. The broad regulation of neuropeptide synthesis and secretion by Creb3l1 presents a new therapeutic strategy for metabolic diseases.
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Affiliation(s)
- Mingkwan Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
| | - Benjamin T Gillard
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
| | - Rizwan Farrukh
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
| | - Alex Paterson
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
| | - Ferdinand Althammer
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.
| | - Valery Grinevich
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Center for Neuroinflammation and Cardiometabolic Diseases, Georgia State University, Atlanta, GA, USA.
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
| | - Michael P Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
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Pauža AG, Mecawi AS, Paterson A, Hindmarch CCT, Greenwood M, Murphy D, Greenwood MP. Osmoregulation of the transcriptome of the hypothalamic supraoptic nucleus: A resource for the community. J Neuroendocrinol 2021; 33:e13007. [PMID: 34297454 DOI: 10.1111/jne.13007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/20/2021] [Indexed: 01/13/2023]
Abstract
The hypothalamic supraoptic nucleus (SON) is a core osmoregulatory control centre that deciphers information about the metabolic state of the organism and orchestrates appropriate homeostatic (endocrine) and allostatic (behavioural) responses. We have used RNA sequencing to describe the polyadenylated transcriptome of the SON of the male Wistar Han rat. These data have been mined to generate comprehensive catalogues of functional classes of genes (enzymes, transcription factors, endogenous peptides, G protein coupled receptors, transporters, catalytic receptors, channels and other pharmacological targets) expressed in this nucleus in the euhydrated state, and that together form the basal substrate for its physiological interactions. We have gone on to show that fluid deprivation for 3 days (dehydration) results in changes in the expression levels of 2247 RNA transcripts, which have similarly been functionally catalogued, and further mined to describe enriched gene categories and putative regulatory networks (Regulons) that may have physiological importance in SON function related plasticity. We hope that the revelation of these genes, pathways and networks, most of which have no characterised roles in the SON, will encourage the neuroendocrine community to pursue new investigations into the new 'known-unknowns' reported in the present study.
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Affiliation(s)
- Audrys G Pauža
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
| | - André Souza Mecawi
- Laboratory of Neuroendocrinology, Department of Biophysics, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Alex Paterson
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
- Bristol Genomics Facility, University of Bristol, Bristol, UK
| | - Charles C T Hindmarch
- Queen's Cardiopulmonary Unit (QCPU), Department of Medicine, Translational Institute of Medicine (TIME), Queen's University, Kingston, ON, Canada
| | - Mingkwan Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
| | - Michael P Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Bristol, UK
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Wang D, Zhang Y, Li J, Dahlgren RA, Wang X, Huang H, Wang H. Risk assessment of cardiotoxicity to zebrafish (Danio rerio) by environmental exposure to triclosan and its derivatives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114995. [PMID: 32554097 DOI: 10.1016/j.envpol.2020.114995] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/02/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
Triclosan (TCS) and its two derivatives (2,4-dichlorophenol and 2,4,6-trichlorophenol) are priority pollutants that coexist in aquatic environments. Joint exposure of TCS, 2,4-dichlorophenol and 2,4,6-trichlorophenol, hereafter referred to as TCS-DT, contributes severe toxicity to aquatic organisms. There is currently a paucity of data regarding TCS-DT molecular toxicity, especially on cardiac diseases. We used zebrafish (Danio rerio) as a model organism, and evaluated the molecular-level cardiotoxicity induced by TCS-DT from embryonic to adult stages. TCS-DT exposure prominently led to phenotypic malformations, such as pericardial cysts, cardiac bleeding, increased SV-BA distance, decreased heart rate and reduced ejection fraction, as well as abnormal swimming behavior. Analyses of the GO and KEGG pathways revealed enrichment pathways related to cardiac development and screened for significantly down-regulated adrenaline signaling in cardiomyocytes. The cardiac marker genes (amhc, cmlc2, vmhc, and nkx2.5) were obtained through protein-protein interaction (PPI) networks, and expressed as down-regulation by WISH. After chronic exposure to TCS-DT from 30 to 90-dpf, both body mass and heart indexes prominently increased, showing myocardial hypertrophy, abnormal heart rate and histopathological injury. Heart tissue damage included disordered and ruptured myocardial fibers, broken and dissolved myofilaments, nuclear pyknosis, mitochondrial injury and inflammatory cell infiltration. Further, abnormal changes in a series of cardiac functions-related biomarkers, including superoxide dismutase, triglyceride, lactate dehydrogenase and creatinine kinase MB, provided evidence for cardiac pathological responses. These results highlight the molecular mechanisms involving TCS-DT induced cardiac toxicity, and provide theoretical data to guide prevention and treatment of pollutant-induced cardiac diseases.
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Affiliation(s)
- Danting Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yuhuan Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jieyi Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, 95616, USA
| | - Xuedong Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, China
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Huili Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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Wu J, He S, Yu Z, Lan D, Xiong X, Li Z. Transcriptomic study of yak mammary gland tissue during lactation. Anim Biotechnol 2020; 33:672-679. [PMID: 32959729 DOI: 10.1080/10495398.2020.1823401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Yak milk, a high-quality milk, is one of the best raw materials for dairy products and economically important to pastoral herdsmen. To make a further understanding of the molecular differences in mammary tissues of the yaks with different milk production during lactation, in this study, we took the use of RNA-seq to perform high-throughput sequencing and analysis of the mammary gland transcriptomes of both high-yielding yak and low-yielding yaks during lactation. By the comparison and analysis of the transcriptome data for the mammary gland tissue of high-yielding yak and low-yield yak, 144 differential genes were screened out, of which 49 were upregulated and 95 were downregulated. Further functional analysis indicated that these differential genes involved in multiple classes based on Gene Ontology (GO) and multiple Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The GO analysis showed that the functions of the differential genes are closely related to the carbohydrate metabolism and other biological processes. KEGG pathway analysis revealed that these genes are mostly enriched in the pathway of antigen processing and presentation, phagosome pathway and type I diabetes pathway and enriched followed by extracellular matrix receptor interaction pathway. Moreover, several other pathways related to amino acid metabolism also showed significant enrichment. Here, the mammary gland transcriptomes of high-yielding yak and low-yielding yaks during lactation have for the first time been compared, and the related differential genes have been screened out and analyzed. Our study paves a way for the further elucidation of the basic molecular mechanism of yak mammary gland tissue, and at the same time provides new ideas for improving the milk production of yaks.
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Affiliation(s)
- Jinbo Wu
- Animal Husbandry Science Institute of ABa Autonomous Prefecture, Hongyuan, P. R. China
| | - Shiming He
- Animal Husbandry Science Institute of ABa Autonomous Prefecture, Hongyuan, P. R. China
| | - Zhonghua Yu
- Animal Husbandry Science Institute of ABa Autonomous Prefecture, Hongyuan, P. R. China
| | - Daoliang Lan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Zhu Li
- Animal Husbandry Science Institute of ABa Autonomous Prefecture, Hongyuan, P. R. China
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Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers. Sci Rep 2020; 10:13281. [PMID: 32764662 PMCID: PMC7411042 DOI: 10.1038/s41598-020-70173-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023] Open
Abstract
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
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10
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Paraskevopoulou S, Dennis AB, Weithoff G, Hartmann S, Tiedemann R. Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto. PLoS One 2019; 14:e0223134. [PMID: 31568501 PMCID: PMC6768451 DOI: 10.1371/journal.pone.0223134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/14/2019] [Indexed: 01/14/2023] Open
Abstract
Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).
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Affiliation(s)
- Sofia Paraskevopoulou
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Unit of Ecology and Ecosystem Modelling, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail:
| | - Alice B. Dennis
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Guntram Weithoff
- Unit of Ecology and Ecosystem Modelling, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefanie Hartmann
- Unit of Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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11
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van den Esker MH, Koets AP. Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis on Mycobacterium avium ssp. paratuberculosis. Vet Sci 2019; 6:vetsci6030059. [PMID: 31247942 PMCID: PMC6789504 DOI: 10.3390/vetsci6030059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/14/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022] Open
Abstract
Mycobacteria cause a wide variety of disease in human and animals. Species that infect ruminants include M. bovis and M. avium ssp. paratuberculosis (MAP). MAP is the causative agent of Johne’s disease in ruminants, which is a chronic granulomatous enteric infection that leads to severe economic losses worldwide. Characteristic of MAP infection is the long, latent phase in which intermittent shedding can take place, while diagnostic tests are unable to reliably detect an infection in this stage. This leads to unnoticed dissemination within herds and the presence of many undetected, silent carriers, which makes the eradication of Johne’s disease difficult. To improve the control of MAP infection, research is aimed at improving early diagnosis. Transcriptomic approaches can be applied to characterize host-pathogen interactions during infection, and to develop novel biomarkers using transcriptional profiles. Studies have focused on the identification of specific RNAs that are expressed in different infection stages, which will assist in the development and clinical implementation of early diagnostic tests.
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Affiliation(s)
- Marielle H van den Esker
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, 8200 AB Lelystad, The Netherlands
| | - Ad P Koets
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, 8200 AB Lelystad, The Netherlands.
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands.
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12
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Slabaugh E, Desai JS, Sartor RC, Lawas LMF, Jagadish SVK, Doherty CJ. Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome. RNA (NEW YORK, N.Y.) 2019; 25:669-684. [PMID: 30872414 PMCID: PMC6521602 DOI: 10.1261/rna.070227.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/06/2019] [Indexed: 05/19/2023]
Abstract
RNA-seq analysis has enabled the evaluation of transcriptional changes in many species including nonmodel organisms. However, in most species only a single reference genome is available and RNA-seq reads from highly divergent varieties are typically aligned to this reference. Here, we quantify the impacts of the choice of mapping genome in rice where three high-quality reference genomes are available. We aligned RNA-seq data from a popular productive rice variety to three different reference genomes and found that the identification of differentially expressed genes differed depending on which reference genome was used for mapping. Furthermore, the ability to detect differentially used transcript isoforms was profoundly affected by the choice of reference genome: Only 30% of the differentially used splicing features were detected when reads were mapped to the more commonly used, but more distantly related reference genome. This demonstrated that gene expression and splicing analysis varies considerably depending on the mapping reference genome, and that analysis of individuals that are distantly related to an available reference genome may be improved by acquisition of new genomic reference material. We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs. We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome analysis.
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Affiliation(s)
- Erin Slabaugh
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jigar S Desai
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Ryan C Sartor
- Crop and Soil Science Department, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Lovely Mae F Lawas
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - S V Krishna Jagadish
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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13
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Nair PS, Kuusi T, Ahvenainen M, Philips AK, Järvelä I. Music-performance regulates microRNAs in professional musicians. PeerJ 2019; 7:e6660. [PMID: 30956902 PMCID: PMC6442922 DOI: 10.7717/peerj.6660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal growth inhibitor, PTEN, and by activating CREB expression and phosphorylation. The up-regulation of microRNAs previously found to be regulators of auditory and nervous system functions (miR-30d, miR-92a and miR-222) is indicative of the sensory perception processes associated with music-performance. Akt signalling pathway which has roles in cell survival, cell differentiation, activation of CREB signalling and dopamine transmission was one of the functions regulated by the up-regulated microRNAs; in accordance with functions identified from songbird learning. The up-regulated microRNAs were also found to be regulators of apoptosis, suggesting repression of apoptotic mechanisms in connection with music-performance. Furthermore, comparative analyses of the target genes of differentially expressed microRNAs with that of the song-responsive microRNAs in songbirds suggest convergent regulatory mechanisms underlying auditory perception.
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Affiliation(s)
| | - Tuire Kuusi
- DocMus Doctoral School, Sibelius Academy, University of the Arts, Helsinki, Finland
| | - Minna Ahvenainen
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Anju K Philips
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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14
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Bhat J, Dubin S, Dananberg A, Quabius ES, Fritsch J, Dowds CM, Saxena A, Chitadze G, Lettau M, Kabelitz D. Histone Deacetylase Inhibitor Modulates NKG2D Receptor Expression and Memory Phenotype of Human Gamma/Delta T Cells Upon Interaction With Tumor Cells. Front Immunol 2019; 10:569. [PMID: 30972064 PMCID: PMC6445873 DOI: 10.3389/fimmu.2019.00569] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
The functional plasticity and anti-tumor potential of human γδ T cells have been widely studied. However, the epigenetic regulation of γδ T-cell/tumor cell interactions has been poorly investigated. In the present study, we show that treatment with the histone deacetylase inhibitor Valproic acid (VPA) significantly enhanced the expression and/or release of the NKG2D ligands MICA, MICB and ULBP-2, but not ULBP-1 in the pancreatic carcinoma cell line Panc89 and the prostate carcinoma cell line PC-3. Under in vitro tumor co-culture conditions, the expression of full length and the truncated form of the NKG2D receptor in γδ T cells was significantly downregulated. Furthermore, using a newly established flow cytometry-based method to analyze histone acetylation (H3K9ac) in γδ T cells, we showed constitutive H3K9aclow and inducible H3K9achigh expression in Vδ2 T cells. The detailed analysis of H3K9aclow Vδ2 T cells revealed a significant reversion of TEMRA to TEM phenotype during in vitro co-culture with pancreatic ductal adenocarcinoma cells. Our study uncovers novel mechanisms of how epigenetic modifiers modulate γδ T-cell differentiation during interaction with tumor cells. This information is important when considering combination therapy of VPA with the γδ T-cell-based immunotherapy for the treatment of certain types of cancer.
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Affiliation(s)
- Jaydeep Bhat
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Samuel Dubin
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alexandra Dananberg
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Elgar Susanne Quabius
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
- Department of Oto-Rhino-Laryngology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Juergen Fritsch
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - C. Marie Dowds
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Ankit Saxena
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Guranda Chitadze
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marcus Lettau
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Dieter Kabelitz
- Institute of Immunology, University Hospital Schleswig-Holstein, Kiel, Germany
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15
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Abstract
The identity of a cell or an organism is at least in part defined by its gene expression and therefore analyzing gene expression remains one of the most frequently performed experimental techniques in molecular biology. The development of the RNA-Sequencing (RNA-Seq) method allows an unprecedented opportunity to analyze expression of protein-coding, noncoding RNA and also de novo transcript assembly of a new species or organism. However, the planning and design of RNA-Seq experiments has important implications for addressing the desired biological question and maximizing the value of the data obtained. In addition, RNA-Seq generates a huge volume of data and accurate analysis of this data involves several different steps and choices of tools. This can be challenging and overwhelming, especially for bench scientists. In this chapter, we describe an entire workflow for performing RNA-Seq experiments. We describe critical aspects of wet lab experiments such as RNA isolation, library preparation and the initial design of an experiment. Further, we provide a step-by-step description of the bioinformatics workflow for different steps involved in RNA-Seq data analysis. This includes power calculations, setting up a computational environment, acquisition and processing of publicly available data if desired, quality control measures, preprocessing steps for the raw data, differential expression analysis, and data visualization. We particularly mention important considerations for each step to provide a guide for designing and analyzing RNA-Seq data.
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16
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Ashbrook DG, Hing B, Michalovicz LT, Kelly KA, Miller JV, de Vega WC, Miller DB, Broderick G, O'Callaghan JP, McGowan PO. Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. J Neuroinflammation 2018; 15:86. [PMID: 29549885 PMCID: PMC5857314 DOI: 10.1186/s12974-018-1113-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/01/2018] [Indexed: 12/12/2022] Open
Abstract
Background Gulf War illness (GWI) is an archetypal, medically unexplained, chronic condition characterised by persistent sickness behaviour and neuroimmune and neuroinflammatory components. An estimated 25–32% of the over 900,000 veterans of the 1991 Gulf War fulfil the requirements of a GWI diagnosis. It has been hypothesised that the high physical and psychological stress of combat may have increased vulnerability to irreversible acetylcholinesterase (AChE) inhibitors leading to a priming of the neuroimmune system. A number of studies have linked high levels of psychophysiological stress and toxicant exposures to epigenetic modifications that regulate gene expression. Recent research in a mouse model of GWI has shown that pre-exposure with the stress hormone corticosterone (CORT) causes an increase in expression of specific chemokines and cytokines in response to diisopropyl fluorophosphate (DFP), a sarin surrogate and irreversible AChE inhibitor. Methods C57BL/6J mice were exposed to CORT for 4 days, and exposed to DFP on day 5, before sacrifice 6 h later. The transcriptome was examined using RNA-seq, and the epigenome was examined using reduced representation bisulfite sequencing and H3K27ac ChIP-seq. Results We show transcriptional, histone modification (H3K27ac) and DNA methylation changes in genes related to the immune and neuronal system, potentially relevant to neuroinflammatory and cognitive symptoms of GWI. Further evidence suggests altered proportions of myelinating oligodendrocytes in the frontal cortex, perhaps connected to white matter deficits seen in GWI sufferers. Conclusions Our findings may reflect the early changes which occurred in GWI veterans, and we observe alterations in several pathways altered in GWI sufferers. These close links to changes seen in veterans with GWI indicates that this model reflects the environmental exposures related to GWI and may provide a model for biomarker development and testing future treatments. Electronic supplementary material The online version of this article (10.1186/s12974-018-1113-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David G Ashbrook
- Department of Biological Sciences and Center for Environmental Epigenetics and Development and Department of Cell and Systems Biology, University of Toronto, Scarborough campus, Toronto, ON, Canada.,Present address: Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38103, USA
| | - Benjamin Hing
- Department of Biological Sciences and Center for Environmental Epigenetics and Development and Department of Cell and Systems Biology, University of Toronto, Scarborough campus, Toronto, ON, Canada.,Present address: Department of Psychiatry, Medical Laboratories, The University of Iowa, Iowa City, Iowa, 52246, USA
| | | | | | - Julie V Miller
- CDC-NIOSH, 1095 Willowdale Road, Morgantown, WV, 26505, USA
| | - Wilfred C de Vega
- Department of Biological Sciences and Center for Environmental Epigenetics and Development and Department of Cell and Systems Biology, University of Toronto, Scarborough campus, Toronto, ON, Canada
| | - Diane B Miller
- CDC-NIOSH, 1095 Willowdale Road, Morgantown, WV, 26505, USA
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital Research Institute, Rochester, NY, USA
| | | | - Patrick O McGowan
- Department of Biological Sciences and Center for Environmental Epigenetics and Development and Department of Cell and Systems Biology, University of Toronto, Scarborough campus, Toronto, ON, Canada. .,Department of Psychology, University of Toronto, Toronto, ON, Canada. .,Department of Physiology, University of Toronto, Toronto, ON, Canada.
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17
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Low JZB, Khang TF, Tammi MT. CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates. BMC Bioinformatics 2017; 18:575. [PMID: 29297307 PMCID: PMC5751784 DOI: 10.1186/s12859-017-1974-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In current statistical methods for calling differentially expressed genes in RNA-Seq experiments, the assumption is that an adjusted observed gene count represents an unknown true gene count. This adjustment usually consists of a normalization step to account for heterogeneous sample library sizes, and then the resulting normalized gene counts are used as input for parametric or non-parametric differential gene expression tests. A distribution of true gene counts, each with a different probability, can result in the same observed gene count. Importantly, sequencing coverage information is currently not explicitly incorporated into any of the statistical models used for RNA-Seq analysis. RESULTS We developed a fast Bayesian method which uses the sequencing coverage information determined from the concentration of an RNA sample to estimate the posterior distribution of a true gene count. Our method has better or comparable performance compared to NOISeq and GFOLD, according to the results from simulations and experiments with real unreplicated data. We incorporated a previously unused sequencing coverage parameter into a procedure for differential gene expression analysis with RNA-Seq data. CONCLUSIONS Our results suggest that our method can be used to overcome analytical bottlenecks in experiments with limited number of replicates and low sequencing coverage. The method is implemented in CORNAS (Coverage-dependent RNA-Seq), and is available at https://github.com/joel-lzb/CORNAS .
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Affiliation(s)
- Joel Z B Low
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia.,Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, University Putra Malaysia, Serdang, 43400, Malaysia
| | - Tsung Fei Khang
- Institute of Mathematical Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,University of Malaya Centre for Data Analytics, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Martti T Tammi
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
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18
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Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification. BMC Genomics 2017; 18:812. [PMID: 29061120 PMCID: PMC5653985 DOI: 10.1186/s12864-017-4161-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/05/2017] [Indexed: 01/30/2023] Open
Abstract
Background Ocean acidification (OA), a change in ocean chemistry due to the absorption of atmospheric CO2 into surface oceans, challenges biogenic calcification in many marine organisms. Ocean acidification is expected to rapidly progress in polar seas, with regions of the Southern Ocean expected to experience severe OA within decades. Biologically, the consequences of OA challenge calcification processes and impose an energetic cost. Results In order to better characterize the response of a polar calcifier to conditions of OA, we assessed differential gene expression in the Antarctic pteropod, Limacina helicina antarctica. Experimental levels of pCO2 were chosen to create both contemporary pH conditions, and to mimic future pH expected in OA scenarios. Significant changes in the transcriptome were observed when juvenile L. h. antarctica were acclimated for 21 days to low-pH (7.71), mid-pH (7.9) or high-pH (8.13) conditions. Differential gene expression analysis of individuals maintained in the low-pH treatment identified down-regulation of genes involved in cytoskeletal structure, lipid transport, and metabolism. High pH exposure led to increased expression and enrichment for genes involved in shell formation, calcium ion binding, and DNA binding. Significant differential gene expression was observed in four major cellular and physiological processes: shell formation, the cellular stress response, metabolism, and neural function. Across these functional groups, exposure to conditions that mimic ocean acidification led to rapid suppression of gene expression. Conclusions Results of this study demonstrated that the transcriptome of the juvenile pteropod, L. h. antarctica, was dynamic and changed in response to different levels of pCO2. In a global change context, exposure of L. h. antarctica to the low pH, high pCO2 OA conditions resulted in a suppression of transcripts for genes involved in key physiological processes: calcification, metabolism, and the cellular stress response. The transcriptomic response at both acute and longer-term acclimation time frames indicated that contemporary L. h. antarctica may not have the physiological plasticity necessary for adaptation to OA conditions expected in future decades. Lastly, the differential gene expression results further support the role of shelled pteropods such as L. h. antarctica as sentinel organisms for the impacts of ocean acidification. Electronic supplementary material The online version of this article (10.1186/s12864-017-4161-0) contains supplementary material, which is available to authorized users.
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19
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Xanthopoulou A, Ganopoulos I, Psomopoulos F, Manioudaki M, Moysiadis T, Kapazoglou A, Osathanunkul M, Michailidou S, Kalivas A, Tsaftaris A, Nianiou-Obeidat I, Madesis P. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers. Gene 2017; 622:50-66. [PMID: 28435133 DOI: 10.1016/j.gene.2017.04.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 01/03/2023]
Abstract
The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits.
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Affiliation(s)
- Aliki Xanthopoulou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Macedonia GR-57001, Greece
| | - Fotis Psomopoulos
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
| | - Maria Manioudaki
- Centre for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Aliki Kapazoglou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sofia Michailidou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Macedonia GR-57001, Greece
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece
| | - Irini Nianiou-Obeidat
- Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece.
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece.
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