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Fatemi SH, Otte ED, Folsom TD, Eschenlauer AC, Roper RJ, Aman JW, Thuras PD. Early Chronic Fluoxetine Treatment of Ts65Dn Mice Rescues Synaptic Vesicular Deficits and Prevents Aberrant Proteomic Alterations. Genes (Basel) 2024; 15:452. [PMID: 38674386 PMCID: PMC11049293 DOI: 10.3390/genes15040452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Down syndrome (DS) is the most common form of inherited intellectual disability caused by trisomy of chromosome 21, presenting with intellectual impairment, craniofacial abnormalities, cardiac defects, and gastrointestinal disorders. The Ts65Dn mouse model replicates many abnormalities of DS. We hypothesized that investigation of the cerebral cortex of fluoxetine-treated trisomic mice may provide proteomic signatures that identify therapeutic targets for DS. Subcellular fractionation of synaptosomes from cerebral cortices of age- and brain-area-matched samples from fluoxetine-treated vs. water-treated trisomic and euploid male mice were subjected to HPLC-tandem mass spectrometry. Analysis of the data revealed enrichment of trisomic risk genes that participate in regulation of synaptic vesicular traffic, pre-synaptic and post-synaptic development, and mitochondrial energy pathways during early brain development. Proteomic analysis of trisomic synaptic fractions revealed significant downregulation of proteins involved in synaptic vesicular traffic, including vesicular endocytosis (CLTA, CLTB, CLTC), synaptic assembly and maturation (EXOC1, EXOC3, EXOC8), anterograde axonal transport (EXOC1), neurotransmitter transport to PSD (SACM1L), endosomal-lysosomal acidification (ROGDI, DMXL2), and synaptic signaling (NRXN1, HIP1, ITSN1, YWHAG). Additionally, trisomic proteomes revealed upregulation of several trafficking proteins, involved in vesicular exocytosis (Rab5B), synapse elimination (UBE3A), scission of endocytosis (DBN1), transport of ER in dendritic spines (MYO5A), presynaptic activity-dependent bulk endocytosis (FMR1), and NMDA receptor activity (GRIN2A). Chronic fluoxetine treatment of Ts65Dn mice rescued synaptic vesicular abnormalities and prevented abnormal proteomic changes in adult Ts65Dn mice, pointing to therapeutic targets for potential treatment of DS.
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Affiliation(s)
- S. Hossein Fatemi
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN 55455, USA;
| | - Elysabeth D. Otte
- Department of Biology, Indiana University, Indianapolis, IN 46202, USA;
| | - Timothy D. Folsom
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA;
| | - Arthur C. Eschenlauer
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Randall J. Roper
- Department of Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA;
| | - Justin W. Aman
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN 55455, USA;
| | - Paul D. Thuras
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School and VA Health Care System, One Veterans Drive, Minneapolis, MN 55417, USA
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Afgan E, Nekrutenko A, Grüning BA, Blankenberg D, Goecks J, Schatz MC, Ostrovsky AE, Mahmoud A, Lonie AJ, Syme A, Fouilloux A, Bretaudeau A, Nekrutenko A, Kumar A, Eschenlauer AC, DeSanto AD, Guerler A, Serrano-Solano B, Batut B, Grüning BA, Langhorst BW, Carr B, Raubenolt BA, Hyde CJ, Bromhead CJ, Barnett CB, Royaux C, Gallardo C, Blankenberg D, Fornika DJ, Baker D, Bouvier D, Clements D, de Lima Morais DA, Tabernero DL, Lariviere D, Nasr E, Afgan E, Zambelli F, Heyl F, Psomopoulos F, Coppens F, Price GR, Cuccuru G, Corguillé GL, Von Kuster G, Akbulut GG, Rasche H, Hotz HR, Eguinoa I, Makunin I, Ranawaka IJ, Taylor JP, Joshi J, Hillman-Jackson J, Goecks J, Chilton JM, Kamali K, Suderman K, Poterlowicz K, Yvan LB, Lopez-Delisle L, Sargent L, Bassetti ME, Tangaro MA, van den Beek M, Čech M, Bernt M, Fahrner M, Tekman M, Föll MC, Schatz MC, Crusoe MR, Roncoroni M, Kucher N, Coraor N, Stoler N, Rhodes N, Soranzo N, Pinter N, Goonasekera NA, Moreno PA, Videm P, Melanie P, Mandreoli P, Jagtap PD, Gu Q, Weber RJM, Lazarus R, Vorderman RHP, Hiltemann S, Golitsynskiy S, Garg S, Bray SA, Gladman SL, Leo S, Mehta SP, Griffin TJ, Jalili V, Yves V, Wen V, Nagampalli VK, Bacon WA, de Koning W, Maier W, Briggs PJ. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 2022; 50:W345-W351. [PMID: 35446428 PMCID: PMC9252830 DOI: 10.1093/nar/gkac247] [Citation(s) in RCA: 250] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 01/19/2023] Open
Abstract
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
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Abstract
Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise. Applications of such sophisticated workflows are many, including those which integrate software from different ‘omic domains (e.g. genomics, proteomics, metabolomics). In these complex workflows, intermediate outputs are often generated as tabular text files, which must be transformed into customized formats which are compatible with the next software tools in the pipeline. Consequently, many text manipulation steps are added to an already complex workflow, overly complicating the process. In some cases, limitations to existing text manipulation are such that desired analyses can only be carried out using highly sophisticated processing steps beyond the reach of even advanced users and developers. For users with some SQL knowledge, these text operations could be combined into single, concise query on a relational database. As a solution, we have developed the Query Tabular Galaxy tool, which leverages a SQLite database generated from tabular input data. This database can be queried and manipulated to produce transformed and customized tabular outputs compatible with downstream processing steps. Regular expressions can also be utilized for even more sophisticated manipulations, such as find and replace and other filtering actions. Using several Galaxy-based multi-omic workflows as an example, we demonstrate how the Query Tabular tool dramatically streamlines and simplifies the creation of multi-step analyses, efficiently enabling complicated textual manipulations and processing. This tool should find broad utility for users of the Galaxy platform seeking to develop and use sophisticated workflows involving text manipulation on tabular outputs.
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Affiliation(s)
- James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, 55904, USA
| | - Caleb Easterly
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Mark Esler
- Department of Horticulture, University of Minnesota, St. Paul, MN, 55108, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Arthur C Eschenlauer
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Department of Horticulture, University of Minnesota, St. Paul, MN, 55108, USA
| | - Adrian D Hegeman
- Department of Horticulture, University of Minnesota, St. Paul, MN, 55108, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
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Johnson JE, Kumar P, Easterly C, Esler M, Mehta S, Eschenlauer AC, Hegeman AD, Jagtap PD, Griffin TJ. Improve your Galaxy text life: The Query Tabular Tool. F1000Res 2018; 7:1604. [PMID: 30519459 PMCID: PMC6248266 DOI: 10.12688/f1000research.16450.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 10/04/2023] Open
Abstract
Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise. Applications of such sophisticated workflows are many, including those which integrate software from different 'omic domains (e.g. genomics, proteomics, metabolomics). In these complex workflows, intermediate outputs are often generated as tabular text files, which must be transformed into customized formats which are compatible with the next software tools in the pipeline. Consequently, many text manipulation steps are added to an already complex workflow, overly complicating the process. In some cases, limitations to existing text manipulation are such that desired analyses can only be carried out using highly sophisticated processing steps beyond the reach of even advanced users and developers. For users with some SQL knowledge, these text operations could be combined into single, concise query on a relational database. As a solution, we have developed the Query Tabular Galaxy tool, which leverages a SQLite database generated from tabular input data. This database can be queried and manipulated to produce transformed and customized tabular outputs compatible with downstream processing steps. Regular expressions can also be utilized for even more sophisticated manipulations, such as find and replace and other filtering actions. Using several Galaxy-based multi-omic workflows as an example, we demonstrate how the Query Tabular tool dramatically streamlines and simplifies the creation of multi-step analyses, efficiently enabling complicated textual manipulations and processing. This tool should find broad utility for users of the Galaxy platform seeking to develop and use sophisticated workflows involving text manipulation on tabular outputs.
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Affiliation(s)
- James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, 55904, USA
| | - Caleb Easterly
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Mark Esler
- Department of Horticulture, University of Minnesota, St. Paul, MN, 55108, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Arthur C. Eschenlauer
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
- Department of Horticulture, University of Minnesota, St. Paul, MN, 55108, USA
| | - Adrian D. Hegeman
- Department of Horticulture, University of Minnesota, St. Paul, MN, 55108, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
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Hahn JJ, Eschenlauer AC, Sleytr UB, Somers DA, Srienc F. Peroxisomes as sites for synthesis of polyhydroxyalkanoates in transgenic plants. Biotechnol Prog 1999; 15:1053-7. [PMID: 10585189 DOI: 10.1021/bp990118n] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial genes responsible for poly(3-hydroxybutyrate) (PHB) biosynthesis were targeted to plant peroxisomes by adding a carboxy-terminal targeting sequence. The enzymes evidently were transported into peroxisomes, retained their catalytic activity, and reacted with peroxisomally available precursors because PHB synthesis in transgenic plant cells was localized to peroxisomes. Up to 2 mg/g fresh weight PHB was produced in suspension cultures of Black Mexican Sweet maize cells after biolistic transformation with three peroxisomally targeted bacterial genes. An equilibrium effect is proposed to explain the unexpected existence of (R)-3-hydroxybutyryl-CoA in plant peroxisomes.
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Affiliation(s)
- J J Hahn
- Department of Chemical Engineering, Biological Process Technology Institute, University of Minnesota, St. Paul, Minnesota 55108, USA
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Hahn JJ, Eschenlauer AC, Narrol MH, Somers DA, Srienc F. Growth kinetics, nutrient uptake, and expression of the Alcaligenes eutrophus poly(beta-hydroxybutyrate) synthesis pathway in transgenic maize cell suspension cultures. Biotechnol Prog 1997; 13:347-54. [PMID: 9265773 DOI: 10.1021/bp970033r] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transgenic suspension cultures of Black Mexican Sweet maize (Zea mays L.) expressing the Alcaligenes eutrophus genes encoding enzymes of the pathway for biosynthesis of the biodegradable polymer poly(beta-hydroxybutyrate) (PHB) were established as a tool for investigating metabolic regulation of the PHB pathway in plant cells. Cultures were grown in a 2 L modified mammalian cell bioreactor and in shake flasks. Biomass doubling times for transgenic bioreactor cultures (3.42 +/- 0.76 days) were significantly higher than those for untransformed cultures (2.01 +/- 0.33 days). Transgenic expression of the bacterial enzymes beta-ketothiolase (0.140 units/mg protein) and acetoacetyl-CoA reductase (0.636 units/mg protein) was detected by enzyme assays and immunoblots. However, over the first 2 years of cultivation, reductase activity decreased to 0.120 units/mg proteins. Furthermore, the PHB synthase gene, although initially present, was not detectable after 1.5 years of cultivation in suspension culture. These facts suggest that transgenic expression of PHB pathway genes in plant cells may not be stable. A hydroxybutyrate derivative was detected via gas chromatography even after 4 years of cultivation. Although the method used to prepare samples for gas chromatography cannot directly distinguish among PHB polymer, hydroxybutyryl-CoA (HB-CoA), and hydroxybutyric acid, solvent washing experiments indicated that most or all of the signal was non-polymeric, presumably H-CoA. The synthesis of HB-CoA appeared to be linked to substrate growth limitation, with HB-CoA accumulation increasing dramatically and cell growth ceasing upon depletion of ammonium. This suggests that the PHB synthesis pathway in plants is subject to regulatory mechanisms similar to those in prokaryotic cells.
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Affiliation(s)
- J J Hahn
- Department of Chemical Engineering and Material Science, University of Minnesota, St. Paul 55108, USA
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Eschenlauer AC, Stoup SK, Srienc F, Somers DA. Production of heteropolymeric polyhydroxyalkanoate in Escherichia coli from a single carbon source. Int J Biol Macromol 1996; 19:121-30. [PMID: 8842775 DOI: 10.1016/0141-8130(96)01114-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Poly[beta-hydroxybutyrate-co-beta-hydroxyvalerate] co-polymer, PHBV, is a polyhydroxyalkanoate (PHA) that has greater utility as a biodegradable thermoplastic polyester than poly-beta-hydroxybutyrate, PHB. In order to produce PHBV, a system of pathways is required to produce both hydroxybutyrate (HB) and hydroxyvalerate (HV) monomers from the sources of carbon. A working model for conversion of glucose to PHBV via acetyl- and propionyl-coenzyme A was constructed by expressing the PHA biosynthesis genes from Alcaligenes eutrophus in Escherichia coli strain K-12 under novel growth conditions. When 1 mM valine was added to 1% glucose medium, growth ceased and up to 2.5% of the incorporated monomers were HV; up to 4% were HV when 1 mM threonine was added as well. Threonine dehydratase (TD) converts threonine to alpha-ketobutyrate; TD is required for HV to be incorporated into PHA unless its transaminated reaction product, alpha-aminobutyrate, is added to the medium. Intracellular alpha-ketobutyrate accumulates when valine is added to the medium because valine, which cannot be metabolized to HV by E. coli strain K-12, stimulates TD and inhibits acetolactate synthase. In turn, alpha-ketobutyrate is converted to propionyl-CoA by the E. coli pyruvate dehydrogenase complex. This constitutes a defined system of pathways for synthesis of a heteropolymeric PHA from a single carbon source, which in the future could be transferred to other organisms including plants.
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Affiliation(s)
- A C Eschenlauer
- Department of Agronomy and Plant Genetics, University of Minnesota-St. Paul 55108-6026, USA
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Abstract
We isolated three Escherichia coli catabolite gene activator protein mutants that are defective in the positive control of transcription initiation from the lac operon promoter region yet retain negative control of transcription from other promoters. One mutant has a substitution of valine for glutamate at residue 72, which lies in the cyclic AMP binding domain and contacts cyclic AMP. The other two mutants have substitutions of asparagine and cysteine for glycine 162, which lies in a surface-exposed turn of the DNA-binding domain. Surprisingly, although all three mutants can repress the lacP2/P3 promoters through the catabolite gene activator protein target site of lac, none displays strong dominance over the ability of wild-type catabolite gene activator protein to stimulate the lacP1 promoter.
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Affiliation(s)
- A C Eschenlauer
- Department of Biochemistry, University of Wisconsin, Madison 53706
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