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Barboza Bispo R, Teixeira do Amaral A, Pinto VB, de Oliveira Santos T, Jário de Lima V, Rohem Simão B, Fischer A, Naldrett MJ, Alvarez S. Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn ( Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis. J Proteome Res 2024. [PMID: 38648199 DOI: 10.1021/acs.jproteome.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.
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Affiliation(s)
- Rosimeire Barboza Bispo
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Antônio Teixeira do Amaral
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biologia Celular e Tecidual (LBCT), UENF, Centro de Biociências e Biotecnologia (CBB), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Talles de Oliveira Santos
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Valter Jário de Lima
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Bruna Rohem Simão
- Laboratório de Melhoramento Genético Vegetal (LMGV), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), 28.013-602, Campos dos Goytacazes, RJ, Brazil
| | - Anne Fischer
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle Center, 1901 Vine St, University of Nebraska-Lincoln (UNL), Lincoln, Nebraska 68588, United States
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle Center, 1901 Vine St, University of Nebraska-Lincoln (UNL), Lincoln, Nebraska 68588, United States
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, Beadle Center, 1901 Vine St, University of Nebraska-Lincoln (UNL), Lincoln, Nebraska 68588, United States
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Johannsen S, Gierse RM, Krüger A, Edwards RL, Nanna V, Fontana A, Zhu D, Masini T, de Carvalho LP, Poizat M, Kieftenbelt B, Hodge DM, Alvarez S, Bunt D, Lacour A, Shams A, Meissner KA, de Souza EE, Dröge M, van Vliet B, den Hartog J, Hutter MC, Held J, Odom John AR, Wrenger C, Hirsch AKH. High Target Homology Does Not Guarantee Inhibition: Aminothiazoles Emerge as Inhibitors of Plasmodium falciparum. ACS Infect Dis 2024; 10:1000-1022. [PMID: 38367280 DOI: 10.1021/acsinfecdis.3c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
In this study, we identified three novel compound classes with potent activity against Plasmodium falciparum, the most dangerous human malarial parasite. Resistance of this pathogen to known drugs is increasing, and compounds with different modes of action are urgently needed. One promising drug target is the enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) of the methylerythritol 4-phosphate (MEP) pathway for which we have previously identified three active compound classes against Mycobacterium tuberculosis. The close structural similarities of the active sites of the DXPS enzymes of P. falciparum and M. tuberculosis prompted investigation of their antiparasitic action, all classes display good cell-based activity. Through structure-activity relationship studies, we increased their antimalarial potency and two classes also show good metabolic stability and low toxicity against human liver cells. The most active compound 1 inhibits the growth of blood-stage P. falciparum with an IC50 of 600 nM. The results from three different methods for target validation of compound 1 suggest no engagement of DXPS. All inhibitor classes are active against chloroquine-resistant strains, confirming a new mode of action that has to be further investigated.
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Affiliation(s)
- Sandra Johannsen
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, Saarbrücken 66123, Germany
| | - Robin M Gierse
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, Saarbrücken 66123, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Arne Krüger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo-SP 05508-000, Brazil
| | - Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Vittoria Nanna
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
| | - Anna Fontana
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
| | - Di Zhu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | | | - Mael Poizat
- Symeres, Kadijk 3, Groningen 9747 AT, The Netherlands
| | | | - Dana M Hodge
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sophie Alvarez
- Proteomics & Metabolomics Facility, Center for Biotechnology, Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Daan Bunt
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Antoine Lacour
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, Saarbrücken 66123, Germany
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, Saarbrücken 66123, Germany
| | - Kamila Anna Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo-SP 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo-SP 05508-000, Brazil
| | | | | | | | - Michael C Hutter
- Center for Bioinformatics, Saarland University, Campus Building E2.1, Saarbrücken 66123, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstraße 27, Tübingen 72074, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen 72074, Germany
- Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 242 Lambaréné, Gabon
| | - Audrey R Odom John
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo-SP 05508-000, Brazil
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, Saarbrücken 66123, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
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Perez V, Zaobornyj T, Vico T, Vanasco V, Marchini T, Godoy E, Alvarez S, Evelson P, Donato M, Gelpi RJ, D'Annunzio V. Middle-age abolishes cardioprotection conferred by thioredoxin-1 in mice. Arch Biochem Biophys 2024; 753:109880. [PMID: 38171410 DOI: 10.1016/j.abb.2023.109880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
Thioredoxin-1 (Trx1) has cardioprotective effects on ischemia/reperfusion (I/R) injury, although its role in ischemic postconditioning (PostC) in middle-aged mice is not understood. This study aimed to evaluate if combining two cardioprotective strategies, such as Trx1 overexpression and PostC, could exert a synergistic effect in reducing infarct size in middle-aged mice. Young or middle-aged wild-type mice (Wt), transgenic mice overexpressing Trx1, and dominant negative (DN-Trx1) mutant of Trx1 mice were used. Mice hearts were subjected to I/R or PostC protocol. Infarct size, hydrogen peroxide (H2O2) production, protein nitration, Trx1 activity, mitochondrial function, and Trx1, pAkt and pGSK3β expression were measured. PostC could not reduce infarct size even in the presence of Trx1 overexpression in middle-aged mice. This finding was accompanied by a lack of Akt and GSK3β phosphorylation, and Trx1 expression (in Wt group). Trx1 activity was diminished and H2O2 production and protein nitration were increased in middle-age. The respiratory control rate dropped after I/R in Wt-Young and PostC restored this value, but not in middle-aged groups. Our results showed that Trx1 plays a key role in the PostC protection mechanism in young but not middle-aged mice, even in the presence of Trx1 overexpression.
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Affiliation(s)
- V Perez
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - T Zaobornyj
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - T Vico
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - V Vanasco
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - T Marchini
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - E Godoy
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - S Alvarez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - P Evelson
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - M Donato
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - R J Gelpi
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - V D'Annunzio
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina.
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Hayer SS, Conrin M, French JA, Benson AK, Alvarez S, Cooper K, Fischer A, Alsafwani ZW, Gasper W, Suhr Van Haute MJ, Hassenstab HR, Azadmanesh S, Briardy M, Gerbers S, Jabenis A, Thompson JL, Clayton JB. Antibiotic-induced gut dysbiosis elicits gut-brain axis relevant multi-omic signatures and behavioral and neuroendocrine changes in a nonhuman primate model. Gut Microbes 2024; 16:2305476. [PMID: 38284649 PMCID: PMC10826635 DOI: 10.1080/19490976.2024.2305476] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Emerging evidence indicates that antibiotic-induced dysbiosis can play an etiological role in the pathogenesis of neuropsychiatric disorders. However, most of this evidence comes from rodent models. The objective of this study was to evaluate if antibiotic-induced gut dysbiosis can elicit changes in gut metabolites and behavior indicative of gut-brain axis disruption in common marmosets (Callithrix jacchus) - a nonhuman primate model often used to study sociability and stress. We were able to successfully induce dysbiosis in marmosets using a custom antibiotic cocktail (vancomycin, enrofloxacin and neomycin) administered orally for 28 days. This gut dysbiosis altered gut metabolite profiles, behavior, and stress reactivity. Increase in gut Fusobacterium spp. post-antibiotic administration was a novel dysbiotic response and has not been observed in any rodent or human studies to date. There were significant changes in concentrations of several gut metabolites which are either neurotransmitters (e.g., GABA and serotonin) or have been found to be moderators of gut-brain axis communication in rodent models (e.g., short-chain fatty acids and bile acids). There was an increase in affiliative behavior and sociability in antibiotic-administered marmosets, which might be a coping mechanism in response to gut dysbiosis-induced stress. Increase in urinary cortisol levels after multiple stressors provides more definitive proof that this model of dysbiosis may cause disrupted communication between gut and brain in common marmosets. This study is a first attempt to establish common marmosets as a novel model to study the impact of severe gut dysbiosis on gut-brain axis cross-talk and behavior.
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Affiliation(s)
- Shivdeep S. Hayer
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Mackenzie Conrin
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Jeffrey A. French
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Program in Neuroscience and Behavior, University of Nebraska at Omaha, Omaha, NE, USA
| | - Andrew K. Benson
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kathryn Cooper
- School of Interdisciplinary Informatics, College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Anne Fischer
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zahraa Wajih Alsafwani
- School of Interdisciplinary Informatics, College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - William Gasper
- School of Interdisciplinary Informatics, College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Mallory J. Suhr Van Haute
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Haley R. Hassenstab
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Shayda Azadmanesh
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Missy Briardy
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Skyler Gerbers
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Aliyah Jabenis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Jennifer L. Thompson
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
| | - Jonathan B. Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
- Callitrichid Research Center, University of Nebraska at Omaha, Omaha, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA
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5
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Liu B, Nguyen PL, Yu H, Li X, Wang H, Price J, Niu M, Guda C, Cheng X, Sun X, Moreau R, Ramer-Tait A, Naldrett MJ, Alvarez S, Yu J. Critical contributions of protein cargos to the functions of macrophage-derived extracellular vesicles. J Nanobiotechnology 2023; 21:352. [PMID: 37770932 PMCID: PMC10537535 DOI: 10.1186/s12951-023-02105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Macrophages are highly plastic innate immune cells that play key roles in host defense, tissue repair, and homeostasis maintenance. In response to divergent stimuli, macrophages rapidly alter their functions and manifest a wide polarization spectrum with two extremes: M1 or classical activation and M2 or alternative activation. Extracellular vesicles (EVs) secreted from differentially activated macrophages have been shown to have diverse functions, which are primarily attributed to their microRNA cargos. The role of protein cargos in these EVs remains largely unexplored. Therefore, in this study, we focused on the protein cargos in macrophage-derived EVs. RESULTS Naïve murine bone marrow-derived macrophages were treated with lipopolysaccharide or interlukin-4 to induce M1 or M2 macrophages, respectively. The proteins of EVs and their parental macrophages were subjected to quantitative proteomics analyses, followed by bioinformatic analyses. The enriched proteins of M1-EVs were involved in proinflammatory pathways and those of M2-EVs were associated with immunomodulation and tissue remodeling. The signature proteins of EVs shared a limited subset of the proteins of their respective progenitor macrophages, but they covered many of the typical pathways and functions of their parental cells, suggesting their respective M1-like and M2-like phenotypes and functions. Experimental examination validated that protein cargos in M1- or M2-EVs induced M1 or M2 polarization, respectively. More importantly, proteins in M1-EVs promoted viability, proliferation, and activation of T lymphocytes, whereas proteins in M2-EVs potently protected the tight junction structure and barrier integrity of epithelial cells from disruption. Intravenous administration of M2-EVs in colitis mice led to their accumulation in the colon, alleviation of colonic inflammation, promotion of M2 macrophage polarization, and improvement of gut barrier functions. Protein cargos in M2-EVs played a key role in their protective function in colitis. CONCLUSION This study has yielded a comprehensive unbiased dataset of protein cargos in macrophage-derived EVs, provided a systemic view of their potential functions, and highlighted the important engagement of protein cargos in the pathophysiological functions of these EVs.
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Affiliation(s)
- Baolong Liu
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 230 Filley Hall, Lincoln, NE, 68583, USA
| | - Phuong Linh Nguyen
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 230 Filley Hall, Lincoln, NE, 68583, USA
| | - Han Yu
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 230 Filley Hall, Lincoln, NE, 68583, USA
| | - Xingzhi Li
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 230 Filley Hall, Lincoln, NE, 68583, USA
| | - Huiren Wang
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 230 Filley Hall, Lincoln, NE, 68583, USA
| | - Jeffrey Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, 260 Food Innovation Center, Lincoln, NE, 68588, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, 115 Food Innovation Center, Lincoln, NE, 68588, USA
| | - Meng Niu
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Xiao Cheng
- Department of Biochemistry, University of Nebraska-Lincoln, N158 Beadle Center, Lincoln, NE, 68588-0665, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, N158 Beadle Center, Lincoln, NE, 68588-0665, USA
| | - Regis Moreau
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 316E Ruth Leverton Hall, Lincoln, NE, 68583, USA
| | - Amanda Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, 260 Food Innovation Center, Lincoln, NE, 68588, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, 115 Food Innovation Center, Lincoln, NE, 68588, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jiujiu Yu
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 230 Filley Hall, Lincoln, NE, 68583, USA.
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6
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Palmer NA, Alvarez S, Naldrett MJ, Muhle A, Sarath G, Edmé SJ, Tatineni S, Mitchell RB, Yuen G. Dynamic Reconfiguration of Switchgrass Proteomes in Response to Rust ( Puccinia novopanici) Infection. Int J Mol Sci 2023; 24:14630. [PMID: 37834079 PMCID: PMC10572835 DOI: 10.3390/ijms241914630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) can be infected by the rust pathogen (Puccinia novopanici) and results in lowering biomass yields and quality. Label-free quantitative proteomics was conducted on leaf extracts harvested from non-infected and infected plants from a susceptible cultivar (Summer) at 7, 11, and 18 days after inoculation (DAI) to follow the progression of disease and evaluate any plant compensatory mechanisms to infection. Some pustules were evident at 7 DAI, and their numbers increased with time. However, fungal DNA loads did not appreciably change over the course of this experiment in the infected plants. In total, 3830 proteins were identified at 1% false discovery rate, with 3632 mapped to the switchgrass proteome and 198 proteins mapped to different Puccinia proteomes. Across all comparisons, 1825 differentially accumulated switchgrass proteins were identified and subjected to a STRING analysis using Arabidopsis (A. thaliana L.) orthologs to deduce switchgrass cellular pathways impacted by rust infection. Proteins associated with plastid functions and primary metabolism were diminished in infected Summer plants at all harvest dates, whereas proteins associated with immunity, chaperone functions, and phenylpropanoid biosynthesis were significantly enriched. At 18 DAI, 1105 and 151 proteins were significantly enriched or diminished, respectively. Many of the enriched proteins were associated with mitigation of cellular stress and defense.
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Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Sophie Alvarez
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Michael J. Naldrett
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Anthony Muhle
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
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Can H, Chanumolu SK, Nielsen BD, Alvarez S, Naldrett MJ, Ünlü G, Otu HH. Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge. Cells 2023; 12:1998. [PMID: 37566077 PMCID: PMC10417344 DOI: 10.3390/cells12151998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023] Open
Abstract
Multi-omics has the promise to provide a detailed molecular picture of biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimal structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to have a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30 °C and 37 °C and obtained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites, suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofaciens at 37 °C.
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Affiliation(s)
- Handan Can
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Sree K. Chanumolu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Barbara D. Nielsen
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Michael J. Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Gülhan Ünlü
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, ID 83844, USA
- School of Food Science, Washington State University, Pullman, WA 99164, USA
| | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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8
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Heinis FI, Alvarez S, Andrews MT. Mass spectrometry of the white adipose metabolome in a hibernating mammal reveals seasonal changes in alternate fuels and carnitine derivatives. Front Physiol 2023; 14:1214087. [PMID: 37449012 PMCID: PMC10337995 DOI: 10.3389/fphys.2023.1214087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
Mammalian hibernators undergo substantial changes in metabolic function throughout the seasonal hibernation cycle. We report here the polar metabolomic profile of white adipose tissue isolated from active and hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus). Polar compounds in white adipose tissue were extracted from five groups representing different timepoints throughout the seasonal activity-torpor cycle and analyzed using hydrophilic interaction liquid chromatography-mass spectrometry in both the positive and negative ion modes. A total of 224 compounds out of 660 features detected after curation were annotated. Unsupervised clustering using principal component analysis revealed discrete clusters representing the different seasonal timepoints throughout hibernation. One-way analysis of variance and feature intensity heatmaps revealed metabolites that varied in abundance between active and torpid timepoints. Pathway analysis compared against the KEGG database demonstrated enrichment of amino acid metabolism, purine metabolism, glycerophospholipid metabolism, and coenzyme A biosynthetic pathways among our identified compounds. Numerous carnitine derivatives and a ketone that serves as an alternate fuel source, beta-hydroxybutyrate (BHB), were among molecules found to be elevated during torpor. Elevated levels of the BHB-carnitine conjugate during torpor suggests the synthesis of beta-hydroxybutyrate in white adipose mitochondria, which may contribute directly to elevated levels of circulating BHB during hibernation.
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Affiliation(s)
- Frazer I. Heinis
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Matthew T. Andrews
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, United States
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Dunigan DD, Agarkova IV, Esmael A, Alvarez S, Van Etten JLV. Early-Phase Drive to the Precursor Pool: Chloroviruses Dive into the Deep End of Nucleotide Metabolism. Viruses 2023; 15:v15040911. [PMID: 37112891 PMCID: PMC10142491 DOI: 10.3390/v15040911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Viruses face many challenges on their road to successful replication, and they meet those challenges by reprogramming the intracellular environment. Two major issues challenging Paramecium bursaria chlorella virus 1 (PBCV-1, genus Chlorovirus, family Phycodnaviridae) at the level of DNA replication are (i) the host cell has a DNA G+C content of 66%, while the virus is 40%; and (ii) the initial quantity of DNA in the haploid host cell is approximately 50 fg, yet the virus will make approximately 350 fg of DNA within hours of infection to produce approximately 1000 virions per cell. Thus, the quality and quantity of DNA (and RNA) would seem to restrict replication efficiency, with the looming problem of viral DNA synthesis beginning in only 60–90 min. Our analysis includes (i) genomics and functional annotation to determine gene augmentation and complementation of the nucleotide biosynthesis pathway by the virus, (ii) transcriptional profiling of these genes, and (iii) metabolomics of nucleotide intermediates. The studies indicate that PBCV-1 reprograms the pyrimidine biosynthesis pathway to rebalance the intracellular nucleotide pools both qualitatively and quantitatively, prior to viral DNA amplification, and reflects the genomes of the progeny virus, providing a successful road to virus infection.
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Affiliation(s)
- David D. Dunigan
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - Irina V. Agarkova
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - Ahmed Esmael
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha 13511, Egypt
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588-0665, USA
| | - James L. Van Van Etten
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
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10
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Zakeri M, Alvarez S, Sansgiry S. Knowledge and Behavior Regarding Cognitive Brain Health in a US sample. Res Social Adm Pharm 2023. [DOI: 10.1016/j.sapharm.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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11
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Grzybowski MW, Zwiener M, Jin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC. Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC Plant Biol 2022; 22:433. [PMID: 36076172 PMCID: PMC9461132 DOI: 10.1186/s12870-022-03823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited. RESULTS Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions. CONCLUSION Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsw, Poland.
| | - Mackenzie Zwiener
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Hongyu Jin
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Nuwan K Wijewardane
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - Abbas Atefi
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, USA
- California Strawberry Commission, San Luis Obispo, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, USA
| | - Yufeng Ge
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA.
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Mansfield A, Reddy Mallareddy J, Yang L, Lin WH, Feathers R, Ayers-Ringler J, Tolosa E, Kizhake S, Kubica S, Boghean L, Alvarez S, Naldrett M, Singh S, Rana S, Zahid M, Smadbeck J, Johnson S, Harris F, Sotiriou S, Karagouga G, McCune A, Schaefer-Klein J, Quiñones-Hinojosa A, Roden A, Kosari F, Cheville J, Vasmatzis G, Anastasiadis P, Borad M, Natarajan A. P2.14-03 Restored Ubiquitination and Degradation of Exon 14 Skipped MET with Proteolysis Targeting Chimeras. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Wang P, Lopes LD, Lopez-Guerrero MG, van Dijk K, Alvarez S, Riethoven JJ, Schachtman DP. Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes. J Exp Bot 2022; 73:5052-5066. [PMID: 35552399 DOI: 10.1093/jxb/erac202] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Root exudates are important for shaping root-associated microbiomes. However, studies on a wider range of metabolites in exudates are required for a comprehensive understanding about their influence on microbial communities. We identified maize inbred lines that differ in exudate concentrations of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and γ-aminobutyric acid (GABA) using a semi-hydroponic system. These lines were grown in the field to determine the changes in microbial diversity and gene expression due to varying concentrations of DIMBOA and GABA in exudates using 16S rRNA amplicon sequencing and metatranscriptomics. Results showed individual and interaction effects of DIMBOA and GABA on the rhizosphere and root endosphere β-diversity, most strongly at the V10 growth stage. The main bacterial families affected by both compounds were Ktedonobacteraceae and Xanthomonadaceae. Higher concentrations of DIMBOA in exudates affected the rhizosphere metatranscriptome, enriching for metabolic pathways associated with plant disease. This study validated the use of natural variation within plant species as a powerful approach for understanding the role of root exudates on microbiome selection. We also showed that a semi-hydroponic system can be used to identify maize genotypes that differ in GABA and DIMBOA exudate concentrations under field conditions. The impact of GABA exudation on root-associated microbiomes is shown for the first time.
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Affiliation(s)
- Peng Wang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lucas Dantas Lopes
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Karin van Dijk
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sophie Alvarez
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jean-Jack Riethoven
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Bioinformatics Core Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Daniel P Schachtman
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
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14
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Gomez-Pinedo U, Matías-Guiu JA, Torre-Fuentes L, Montero-Escribano P, Hernández-Lorenzo L, Pytel V, Maietta P, Alvarez S, Sanclemente-Alamán I, Moreno-Jimenez L, Ojeda-Hernandez D, Villar-Gómez N, Benito-Martin MS, Selma-Calvo B, Vidorreta-Ballesteros L, Madrid R, Matías-Guiu J. Variant rs4149584 (R92Q) of the TNFRSF1A gene in patients with familial multiple sclerosis. Neurologia 2022:S2173-5808(22)00087-6. [PMID: 35963536 DOI: 10.1016/j.nrleng.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Genomic studies have identified numerous genetic variants associated with susceptibility to multiple sclerosis (MS); however, each one explains only a small percentage of the risk of developing the disease. These variants are located in genes involved in specific pathways, which supports the hypothesis that the risk of developing MS may be linked to alterations in these pathways, rather than in specific genes. We analyzed the role of the TNFRSF1A gene, which encodes one of the TNF-α receptors involved in a signaling pathway previously linked to autoimmune disease. METHODS We included 138 individuals from 23 families including at least 2 members with MS, and analyzed the presence of exonic variants of TNFRSF1A through whole-exome sequencing. We also conducted a functional study to analyze the pathogenic mechanism of variant rs4149584 (-g.6442643C > G, NM_001065.4:c.362 G > A, R92Q) by plasmid transfection into human oligodendroglioma (HOG) cells, which behave like oligodendrocyte lineage cells; protein labeling was used to locate the protein within cells. We also analyzed the ability of transfected HOG cells to proliferate and differentiate into oligodendrocytes. RESULTS Variant rs4149584 was found in 2 patients with MS (3.85%), one patient with another autoimmune disease (7.6%), and in 5 unaffected individuals (7.46%). The 2 patients with MS and variant rs4149584 were homozygous carriers and belonged to the same family, whereas the remaining individuals presented the variant in heterozygosis. The study of HOG cells transfected with the mutation showed that the protein does not reach the cell membrane, but rather accumulates in the cytoplasm, particularly in the endoplasmic reticulum and near the nucleus; this suggests that, in the cells presenting the mutation, TNFRSF1 does not act as a transmembrane protein, which may alter its signaling pathway. The study of cell proliferation and differentiation found that transfected cells continue to be able to differentiate into oligodendrocytes and are probably still capable of producing myelin, although they present a lower rate of proliferation than wild-type cells. CONCLUSIONS Variant rs4149584 is associated with risk of developing MS. We analyzed its functional role in oligodendrocyte lineage cells and found an association with MS in homozygous carriers. However, the associated molecular alterations do not influence the differentiation into oligodendrocytes; we were therefore unable to confirm whether this variant alone is pathogenic in MS, at least in heterozygosis.
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Affiliation(s)
- U Gomez-Pinedo
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain.
| | - J A Matías-Guiu
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - L Torre-Fuentes
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - P Montero-Escribano
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - L Hernández-Lorenzo
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - V Pytel
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain; Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | - I Sanclemente-Alamán
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - L Moreno-Jimenez
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - D Ojeda-Hernandez
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - N Villar-Gómez
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - M S Benito-Martin
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - B Selma-Calvo
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - L Vidorreta-Ballesteros
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | | | - J Matías-Guiu
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain; Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
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15
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Grover S, Cardona JB, Zogli P, Alvarez S, Naldrett MJ, Sattler SE, Louis J. Reprogramming of sorghum proteome in response to sugarcane aphid infestation. Plant Sci 2022; 320:111289. [PMID: 35643611 DOI: 10.1016/j.plantsci.2022.111289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Sugarcane aphid (SCA; Melanaphis sacchari Zehntner) is a key piercing-sucking pest of sorghum (Sorghum bicolor) that cause significant yield losses. While feeding on host plants, complex signaling networks are invoked from recognition of insect attack to induction of plant defenses. Consequently, these signaling networks lead to the production of insecticidal compounds or limited access of nutrients to insects. Previously, several studies were published on the transcriptomics analysis of sorghum in response to SCA infestation, but no information is available on the physiological changes of sorghum at the proteome level. We used the SCA resistant sorghum genotype SC265 for the global proteomics analysis after 1 and 7 days of SCA infestation using the TMT-plex technique. Peptides matching a total of 4211 proteins were identified and 158 proteins were differentially expressed at day 1 and 7. Overall, proteome profiling of SC265 after SCA infestation at days 1 and 7 revealed the suppression of plant defense-related proteins and upregulation of plant defense and signaling-related proteins, respectively. The plant defense responses based on proteome data were validated using electrical penetration graph (EPG) technique to observe changes in aphid feeding. Feeding behavior analyses revealed that SCA spent significantly longer time in phloem phase on SCA infested plants for day 1 and lesser time in day 7 SCA infested sorghum plants, compared to their respective control plants. Overall, our study provides insights into underlying mechanisms that contribute to sorghum resistance to SCA.
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Affiliation(s)
- Sajjan Grover
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | | | - Prince Zogli
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, US Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583, USA
| | - Joe Louis
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln NE 68583, USA.
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16
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Ray S, Chee L, Zhou Y, Schaefer MA, Naldrett MJ, Alvarez S, Woods NT, Hewitt K. Functional requirements for a Samd14-capping protein complex in stress erythropoiesis. eLife 2022; 11:76497. [PMID: 35713400 PMCID: PMC9282853 DOI: 10.7554/elife.76497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Acute anemia induces rapid expansion of erythroid precursors and accelerated differentiation to replenish erythrocytes. Paracrine signals—involving cooperation between stem cell factor (SCF)/Kit signaling and other signaling inputs—are required for the increased erythroid precursor activity in anemia. Our prior work revealed that the sterile alpha motif (SAM) domain 14 (Samd14) gene increases the regenerative capacity of the erythroid system in a mouse genetic model and promotes stress-dependent Kit signaling. However, the mechanism underlying Samd14’s role in stress erythropoiesis is unknown. We identified a protein-protein interaction between Samd14 and the α- and β-heterodimers of the F-actin capping protein (CP) complex. Knockdown of the CP β subunit increased erythroid maturation in murine ex vivo cultures and decreased colony forming potential of stress erythroid precursors. In a genetic complementation assay for Samd14 activity, our results revealed that the Samd14-CP interaction is a determinant of erythroid precursor cell levels and function. Samd14-CP promotes SCF/Kit signaling in CD71med spleen erythroid precursors. Given the roles of Kit signaling in hematopoiesis and Samd14 in Kit pathway activation, this mechanism may have pathological implications in acute/chronic anemia. Anemia is a condition in which the body has a shortage of healthy red blood cells to carry enough oxygen to support its organs. A range of factors are known to cause anemia, including traumatic blood loss, toxins or nutritional deficiency. An estimated one-third of all women of reproductive age are anemic, which can cause tiredness, weakness and shortness of breath. Severe anemia drives the release of hormones and growth factors, leading to a rapid regeneration of precursor red blood cells to replenish the supply in the blood. To understand how red blood cell regeneration is controlled, Ray et al. studied proteins involved in regenerating blood using mice in which anemia had been induced with chemicals. Previous research had shown that the protein Samd14 is produced at higher quantities in individuals with anemia, and is involved with the recovery of lost red blood cells. However, it is not known how the Samd14 protein plays a role in regenerating blood cells, or whether Samd14 interacts with other proteins required for red blood cell production. To shed light on these questions, mouse cells exposed to anemia conditions were used to see what proteins Samd14 binds to. Purifying Samd14 revealed that it interacts with the actin capping protein. This interaction relies on a specific region of Samd14 that is similar to regions in other proteins that bind capping proteins. Ray et al. found that the interaction between Samd14 and the actin capping protein increased the signals needed for the development and survival of new red blood cells. These results identify a signaling mechanism that, if disrupted, could cause anemia to develop. They lead to a better understanding of how our bodies recover from anemia, and potential avenues to treat this condition.
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Affiliation(s)
- Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, United States
| | - Linda Chee
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, United States
| | - Yichao Zhou
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, United States
| | - Meg A Schaefer
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, United States
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, University of Nebraska-Lincoln, Lincoln, United States
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, University of Nebraska-Lincoln, Lincoln, United States
| | - Nicholas T Woods
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, United States
| | - Kyle Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, United States
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Lopez-Guerrero MG, Wang P, Phares F, Schachtman DP, Alvarez S, van Dijk K. A glass bead semi-hydroponic system for intact maize root exudate analysis and phenotyping. Plant Methods 2022; 18:25. [PMID: 35246193 PMCID: PMC8897885 DOI: 10.1186/s13007-022-00856-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage. RESULTS This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl2, and to measure root phenotype data using standard methods and the Digital imaging of root traits (DIRT) software. LC-MS/MS (Liquid Chromatography-Tandem Mass Spectrometry) and GC-MS (Gas Chromatography-Mass Spectrometry) targeted metabolomics platforms were used to detect and quantify metabolites in the root exudates. Phytohormones, some of which are reported in maize root exudates for the first time, the benzoxazinoid DIMBOA (2,4-Dihydroxy-7-methoxy-1,4-benzoxazin-3-one), amino acids, and sugars were detected and quantified. After validating the methodology using known concentrations of standards for the targeted compounds, we found that the choice of the exudate collection solution affected the exudation and analysis of a subset of analyzed metabolites. No differences between collection in water or CaCl2 were found for phytohormones and sugars. In contrast, the amino acids were more concentrated when water was used as the exudate collection solution. The collection in CaCl2 required a clean-up step before MS analysis which was found to interfere with the detection of a subset of the amino acids. Finally, using the phenotypic measurements and the metabolite data, significant differences between genotypes were found and correlations between metabolites and phenotypic traits were identified. CONCLUSIONS A new plant growth system combining glass beads supported hydroponics with semi-automated drip irrigation of sterile solutions was implemented to grow maize plants and collect root exudates without disturbing or damaging the roots. The validated targeted exudate metabolomics platform combined with root phenotyping provides a powerful tool to link plant root and exudate phenotypes to genotype and study the natural variation of plant populations.
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Affiliation(s)
| | - Peng Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Felicia Phares
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Sophie Alvarez
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Karin van Dijk
- Biochemistry Department, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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18
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Balaji P, Toan Tran V, Barry AM, Yang E, Lu J, Bandodkar S, Alvarez S, Ronquillo J, Varikatt W, McEwan A, Thiagalingam A, Thomas P, Qian C. Differential Biophysics of Heating, Efficacy and Durability of Renal Denervation for Microwave and Radiofrequency Ablation. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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19
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Balaji P, Toan TV, Barry A, Yang E, Lu J, Bandodkar S, Alvarez S, Ronquillo J, Varikatt W, McEwan A, Thiagalingam A, P. Thomas S, C. Qian P. Long-Term Safety and Efficacy of Transcatheter Microwave Renal Denervation in an Ovine Model. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Nolasco E, Naldrett M, Alvarez S, Johnson PE, Majumder K. Bioactivity of Cooked Standard and Enriched Whole Eggs from White Leghorn and Rhode Island Red in Exhibiting In-Vitro Antioxidant and ACE-Inhibitory Effects. Nutrients 2021; 13:4232. [PMID: 34959785 PMCID: PMC8705232 DOI: 10.3390/nu13124232] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Hen breed, diet enrichment, cooking methods, and gastrointestinal (GI) digestion modulates the bioaccessibility of the bioactive compounds in eggs, but their synergistic role in modulating bioactivity is still unclear. The present study evaluates the effect of hen breed, diet enrichment, and GI digestion on the cooked whole egg-derived peptides in-vitro antioxidant and antihypertensive activities. Standard and enriched whole eggs from White Leghorn (WLH) and Rhode Island Red (RIR) hens were boiled or fried and subjected to GI digestion. Antioxidant activity was measured through oxygen radical absorbance capacity (ORAC) and gastrointestinal epithelial cell-based assays, and the antihypertensive capacity by in-vitro Angiotensin-I Converting Enzyme (ACE) inhibition assay. WLH fried standard egg hydrolysate showed a high ORAC antioxidant activity but failed to show any significant antioxidant effect in the cell-based assay. No significant differences were observed in the antihypertensive activity, although enriched samples tended to have a higher ACE-inhibitory capacity. The peptide profile explained the antioxidant capacities based on antioxidant structural requirements from different peptide fractions, while previously reported antihypertensive peptides were found in all samples. The study validates the importance of physiologically relevant models and requires future studies to confirm mechanisms that yield bioactive compounds in whole egg hydrolysates.
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Affiliation(s)
- Emerson Nolasco
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA; (E.N.); (P.E.J.)
| | - Mike Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588-0665, USA; (M.N.); (S.A.)
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588-0665, USA; (M.N.); (S.A.)
| | - Philip E. Johnson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA; (E.N.); (P.E.J.)
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA; (E.N.); (P.E.J.)
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21
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Bandyopadhyay M, Guha S, Naldrett MJ, Alvarez S, Majumder K. Evaluating the effect of high-pressure processing in contrast to boiling on the antioxidant activity from alcalase hydrolysate of Great Northern Beans (Phaseolus vulgaris). J Food Biochem 2021; 45:e14004. [PMID: 34792196 DOI: 10.1111/jfbc.14004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Food processing can alter protein structure, modulate enzyme accessibility, and therefore the release of bioactive peptides. Thus, processing techniques, boiling, high-pressure processing (HPP), and a combination of both, were compared for their efficiency to release antioxidant peptides after alcalase hydrolysis of Great Northern Beans (GNBs). The oxygen radical absorbance capacity (ORAC) indicated that boiled hydrolysates had the highest antioxidant activity (370.9 ± 43.8 µmol TEAC/g). Mass spectrometry-based analysis suggested that di- and tri-peptide expression were significantly altered among the three treatments, and either Ile, Leu, Phe, and Arg containing peptides potentially contributed toward the enhanced antioxidant activity. Furthermore, the total phenolic content of the HPP-treated hydrolysate was higher than the other two treatments, with ferulic acid being the most prominent phenolic compound present in the bean hydrolysates. This study indicates that thermal processing such as boiling is more effective in modulating the release of antioxidant peptides. PRACTICAL APPLICATIONS: Common beans (Phaseolus vulgaris), such as Great Northern Beans (GNBs) are one of the major pulse crops in the United States. Storage proteins in beans can release peptides with biological activities after enzymatic hydrolysis. However, processing conditions can modulate the release of peptides. The present study is primarily focused on comparing the two processing methods, boiling and HPP, and their combination for the generation of peptides with potential antioxidant activity in alcalase-digested GNBs. Data from the study suggest that thermal treatment such as boiling is more effective in modulating the release of peptides from alcalase hydrolysate of GNBs with antioxidant activity. This is particularly important because over different cultures around the world, boiling is the most widely used processing method for the cooking of beans, and hence, these data also ensure that boiling is the most effective method in getting the most beneficial effects from the consumption of beans.
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Affiliation(s)
- Madhurima Bandyopadhyay
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Snigdha Guha
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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22
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Liu B, Li X, Yu H, Shi X, Zhou Y, Alvarez S, Naldrett MJ, Kachman SD, Ro SH, Sun X, Chung S, Jing L, Yu J. Therapeutic potential of garlic chive-derived vesicle-like nanoparticles in NLRP3 inflammasome-mediated inflammatory diseases. Am J Cancer Res 2021; 11:9311-9330. [PMID: 34646372 PMCID: PMC8490522 DOI: 10.7150/thno.60265] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Aberrant activation of the nucleotide-binding domain and leucine-rich repeat related (NLR) family, pyrin domain containing 3 (NLRP3) inflammasome drives the development of many complex inflammatory diseases, such as obesity, Alzheimer's disease, and atherosclerosis. However, no medications specifically targeting the NLRP3 inflammasome have become clinically available. Therefore, we aim to identify new inhibitors of the NLRP3 inflammasome in this study. Methods: Vesicle-like nanoparticles (VLNs) were extracted from garlic chives and other Allium vegetables and their effects on the NLRP3 inflammasome were evaluated in primary macrophages. After garlic chive-derived VLNs (GC-VLNs) were found to exhibit potent anti-NLRP3 inflammasome activity in cell culture, such function was further assessed in a murine acute liver injury disease model, as well as in diet-induced obesity. Finally, GC-VLNs were subjected to omics analysis to identify the active components with anti-NLRP3 inflammasome function. Results: GC-VLNs are membrane-enclosed nanoparticles containing lipids, proteins, and RNAs. They dose-dependently inhibit pathways downstream of NLRP3 inflammasome activation, including caspase-1 autocleavage, cytokine release, and pyroptotic cell death in primary macrophages. The inhibitory effects of GC-VLNs on the NLRP3 inflammasome are specific, considering their marginal impact on activation of other inflammasomes. Local administration of GC-VLNs in mice alleviates NLRP3 inflammasome-mediated inflammation in chemical-induced acute liver injury. When administered orally or intravenously, GC-VLNs accumulate in specific tissues and suppress activation of the NLRP3 inflammasome and chronic inflammation in diet-induced obese mice. The phospholipid 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLPC) in GC-VLNs has been identified to inhibit NLRP3 inflammasome activation. Conclusions: Identification of GC-VLNs and their active component DLPC as potent inflammasome inhibitors provides new therapeutic candidates in the treatment of NLRP3 inflammasome-driven diseases.
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23
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Vu DC, Vu QT, Huynh L, Lin CH, Alvarez S, Vo XT, Nguyen THD. Evaluation of fatty acids, phenolics and bioactivities of spent coffee grounds prepared from Vietnamese coffee. International Journal of Food Properties 2021. [DOI: 10.1080/10942912.2021.1977657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Danh C. Vu
- Faculty of Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Quyen T. Vu
- Faculty of Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Long Huynh
- Faculty of Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Chung-Ho Lin
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, Missouri, United States
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States
| | - Xuyen T. Vo
- Faculty of Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Trang H. D. Nguyen
- Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, Vietnam
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24
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Cepeda–Duque JC, Gómez–Valencia B, Alvarez S, Gutiérrez–Sanabria DR, Lizcano DJ. Daily activity pattern of pumas (Puma concolor) and their potential prey in a tropical cloud forest of Colombia. Anim Biodiv Conserv 2021. [DOI: 10.32800/abc.2021.44.0267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ecosystems in the northern Andes face unprecedented habitat loss. Pumas are the top predators in the region and exert key ecological functions, such as population control and resource facilitation. However, little is known about the temporal niche of the species or its effects on behaviour of prey in the tropics. We hypothesized that there is a link between the activity patterns of pumas and their prey in a cloud forest of the Central Andes of Colombia. We installed 61 camera traps to estimate the degree of overlap between the daily activity curves of pumas and seven potential prey species, using conditional kernel density functions. Pumas, armadillos, mountain pacas, and white–eared opossums were mainly nocturnal, with little crepuscular activity and high temporal overlap. Central American agouti, mountain coati, little red brocket deer, and Cauca guan displayed a predominantly diurnal activity and temporal partitioning with pumas. As opportunistic predators, pumas were able to maximize foraging efficiency by preying on the crepuscular and nocturnal species. Conservation of this highland predator will largely depend on the suitable management of its native prey.
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Affiliation(s)
| | - B. Gómez–Valencia
- Instituto de Investigaciones Alexander von Humboldt, Bogotá, Colombia
| | - S. Alvarez
- Wildlife Conservation Society, Cali, Colombia
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25
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Guha S, Alvarez S, Majumder K. Transport of Dietary Anti-Inflammatory Peptide, γ-Glutamyl Valine (γ-EV), across the Intestinal Caco-2 Monolayer. Nutrients 2021; 13:nu13051448. [PMID: 33923345 PMCID: PMC8145144 DOI: 10.3390/nu13051448] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 01/04/2023] Open
Abstract
The present study analyzed the transepithelial transport of the dietary anti-inflammatory peptide, γ-glutamyl valine (γ-EV). γ-EV is naturally found in dry edible beans. Our previous study demonstrated the anti-inflammatory potency of γ-EV against vascular inflammation at a concentration of 1mM, and that it can transport with the apparent permeability coefficient (Papp) of 1.56 × 10-6 ± 0.7 × 10-6 cm/s across the intestinal Caco-2 cells. The purpose of the current study was to explore whether the permeability of the peptide could be enhanced and to elucidate the mechanism of transport of γ-EV across Caco-2 cells. The initial results indicated that γ-EV was nontoxic to the Caco-2 cells up to 5 mM concentration and could be transported across the intestinal cells intact. During apical-to-basolateral transport, a higher peptide dose (5 mM) significantly (p < 0.01) enhanced the transport rate to 2.5 × 10-6 ± 0.6 × 10-6 cm/s. Cytochalasin-D disintegrated the tight-junction proteins of the Caco-2 monolayer and increased the Papp of γ-EV to 4.36 × 10-6 ± 0.16 × 10-6 cm/s (p < 0.001), while theaflavin 3'-gallate and Gly-Sar significantly decreased the Papp (p < 0.05), with wortmannin having no effects on the peptide transport, indicating that the transport route of γ-EV could be via both PepT1-mediated and paracellular.
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Affiliation(s)
- Snigdha Guha
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA;
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588-0665, USA;
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA;
- Correspondence: ; Tel.: +1-(402)-472-3510; Fax: +1-(402)-472-4474
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26
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King HM, Rana S, Kubica SP, Mallareddy JR, Kizhake S, Ezell EL, Zahid M, Naldrett MJ, Alvarez S, Law HCH, Woods NT, Natarajan A. Aminopyrazole based CDK9 PROTAC sensitizes pancreatic cancer cells to venetoclax. Bioorg Med Chem Lett 2021; 43:128061. [PMID: 33895280 DOI: 10.1016/j.bmcl.2021.128061] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 02/11/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) is a member of the cyclin-dependent kinase (CDK) family which is involved in transcriptional regulation of several genes, including the oncogene Myc, and is a validated target for pancreatic cancer. Here we report the development of an aminopyrazole based proteolysis targeting chimera (PROTAC 2) that selectively degrades CDK9 (DC50 = 158 ± 6 nM). Mass spectrometry-based kinome profiling shows PROTAC 2 selectively degrades CDK9 in MiaPaCa2 cells and sensitizes them to Venetoclax mediated growth inhibition.
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Affiliation(s)
- Hannah M King
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Sandeep Rana
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Sydney P Kubica
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Smitha Kizhake
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Edward L Ezell
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Muhammad Zahid
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Michael J Naldrett
- Proteomics & Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - Sophie Alvarez
- Proteomics & Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - Henry C-H Law
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Nicholas T Woods
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68022, USA
| | - Amarnath Natarajan
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68022, USA; Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68022, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68022, USA.
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27
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Ethèves MA, Choisis N, Alvarez S, Dalleau F, Hascoat J, Gallard V, Cardinale E. Risk factors for Salmonella enterica subsp . enterica persistence in broiler-chicken flocks on Reunion Island. Heliyon 2021; 7:e06278. [PMID: 33748450 PMCID: PMC7969330 DOI: 10.1016/j.heliyon.2021.e06278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/09/2020] [Accepted: 02/09/2021] [Indexed: 11/24/2022] Open
Abstract
This study was conducted to identify the main risk factors for Salmonella spp. persistence in broiler flocks in Reunion Island. Seventy broiler farms were surveyed from March 2016 to June 2018. Samples of fresh droppings were collected using gauze socks, and a questionnaire was completed with the farmers. Persistence was defined as an infection with the same serovar before and after cleaning and disinfection (C/D) of poultry houses. Salmonella spp. was found to persist on 27% of the farms. Cleaning concrete surrounding areas (OR = 0.23) and disinfecting silos (OR = 0.17) reduced the risk of pathogen persistence. An analysis of infections of pests found in the vicinity of the farms confirmed their role in the persistence of Salmonella spp. Fifteen percent of the pests were infected and the presence of mealworms in poultry litter (OR = 6.69) was found to increase the risk of Salmonella spp. persistence. We conclude that improved cleaning-disinfection, sanitary preventive measures and pest control in the poultry sector are needed to avoid the persistence of Salmonella spp. on broiler farms.
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Affiliation(s)
- M A Ethèves
- UMR Animal, Santé, Territoires, Risques et Écosystèmes, CIRAD - BIOS, Cyroi Platform 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France.,ASTRE, Univ Montpellier, CIRAD, INRAe, Montpellier, France
| | - N Choisis
- Groupement de défense sanitaire de La Réunion, 1 rue du Père Hauck, PK23, Bâtiment E/F/G, 97418 La Plaine des Cafres, La Réunion, France
| | - S Alvarez
- UMR Animal, Santé, Territoires, Risques et Écosystèmes, CIRAD - BIOS, Cyroi Platform 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France.,ASTRE, Univ Montpellier, CIRAD, INRAe, Montpellier, France
| | - F Dalleau
- Groupement de défense sanitaire de La Réunion, 1 rue du Père Hauck, PK23, Bâtiment E/F/G, 97418 La Plaine des Cafres, La Réunion, France
| | - J Hascoat
- Groupement de défense sanitaire de La Réunion, 1 rue du Père Hauck, PK23, Bâtiment E/F/G, 97418 La Plaine des Cafres, La Réunion, France
| | - V Gallard
- Coopérative des Aviculteurs de La Réunion, AVIPOLE, 14 rue de l'Etang, 97450 Saint-Louis, La Réunion, France
| | - E Cardinale
- UMR Animal, Santé, Territoires, Risques et Écosystèmes, CIRAD - BIOS, Cyroi Platform 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France.,ASTRE, Univ Montpellier, CIRAD, INRAe, Montpellier, France
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28
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Chen X, Liu B, Li X, An TT, Zhou Y, Li G, Wu‐Smart J, Alvarez S, Naldrett MJ, Eudy J, Kubik G, Wilson RA, Kachman SD, Cui J, Yu J. Identification of anti-inflammatory vesicle-like nanoparticles in honey. J Extracell Vesicles 2021; 10:e12069. [PMID: 33613874 PMCID: PMC7879699 DOI: 10.1002/jev2.12069] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 01/05/2021] [Accepted: 01/31/2021] [Indexed: 12/11/2022] Open
Abstract
Honey has been used as a nutrient, an ointment, and a medicine worldwide for many centuries. Modern research has demonstrated that honey has many medicinal properties, reflected in its anti-microbial, anti-oxidant, and anti-inflammatory bioactivities. Honey is composed of sugars, water and a myriad of minor components, including minerals, vitamins, proteins and polyphenols. Here, we report a new bioactive component‒vesicle-like nanoparticles‒in honey (H-VLNs). These H-VLNs are membrane-bound nano-scale particles that contain lipids, proteins and small-sized RNAs. The presence of plant-originated plasma transmembrane proteins and plasma membrane-associated proteins suggests the potential vesicle-like nature of these particles. H-VLNs impede the formation and activation of the nucleotide-binding domain and leucine-rich repeat related (NLR) family, pyrin domain containing 3 (NLRP3) inflammasome, which is a crucial inflammatory signalling platform in the innate immune system. Intraperitoneal administration of H-VLNs in mice alleviates inflammation and liver damage in the experimentally induced acute liver injury. miR-4057 in H-VLNs was identified in inhibiting NLRP3 inflammasome activation. Together, our studies have identified anti-inflammatory VLNs as a new bioactive agent in honey.
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Affiliation(s)
- Xingyi Chen
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Baolong Liu
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Xingzhi Li
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Thuy T. An
- Department of Computer Science and EngineeringUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - You Zhou
- Center for BiotechnologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Gang Li
- Department of Plant PathologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Judy Wu‐Smart
- Department of EntomologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Sophie Alvarez
- Nebraska Center for Biotechnology, University of Nebraska‐LincolnProteomics and Metabolomics FacilityNebraskaUSA
| | - Michael J. Naldrett
- Nebraska Center for Biotechnology, University of Nebraska‐LincolnProteomics and Metabolomics FacilityNebraskaUSA
| | - James Eudy
- Department of Genetics Cell Biology and AnatomyUniversity of Nebraska Medical Center, 985915 Nebraska Medical CenterOmahaNebraskaUSA
| | - Gregory Kubik
- Genomics Core Facility, University of Nebraska Medical CenterOmahaNebraskaUSA
| | - Richard A. Wilson
- Department of Plant PathologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Stephen D. Kachman
- Department of StatisticsUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Juan Cui
- Department of Computer Science and EngineeringUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Jiujiu Yu
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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Rao PS, Nolasco E, Handa A, Naldrett MJ, Alvarez S, Majumder K. Effect of pH and Heat Treatment on the Antioxidant Activity of Egg White Protein-Derived Peptides after Simulated In-Vitro Gastrointestinal Digestion. Antioxidants (Basel) 2020; 9:antiox9111114. [PMID: 33187320 PMCID: PMC7697783 DOI: 10.3390/antiox9111114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 01/22/2023] Open
Abstract
The study aimed to analyze pH and heat treatment’s effect in modulating the release of peptides with antioxidant activity after simulated gastrointestinal (GI) digestion of Egg white powder (EWP). EWP samples with neutral (EWPN) and alkaline (EWPA) pH were heat-treated at 20, 60, and 90 °C and analyzed for protein aggregation, solubility, and GI digestibility. Heat treatment decreased solubility and induced protein aggregation, which was higher for EWPN as compared to EWPA. The unfolding of EWPA proteins at 60 °C exhibited a higher GI digestibility and antioxidant activity via Oxygen Radical Absorbance Capacity (ORAC) assay as compared to EWPN. Interestingly, a reverse trend was observed in the cellular antioxidant assay, and the GI-digest of EWPN exhibited a higher antioxidant activity. The LC-MS/MS analysis are in concordance with cellular antioxidant activity assay and showed a higher intensity for peptides with potential antioxidant activity in the GI-digest of EWPN. The results indicate that heat treatment but not the pH is a critical factor in improving the protein digestibility and releasing peptides with antioxidant activity after GI digestion.
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Affiliation(s)
- Priyanka Singh Rao
- Dairy Chemistry Division, National Dairy Research Institute (ICAR-NDRI), Karnal, Haryana 132001, India;
| | - Emerson Nolasco
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA;
| | - Akihiro Handa
- Institute of Technology Solution, R&D Division, Kewpie Corporation, 2-5-7 Sengawa, Tokyo 1820002, Japan;
| | - Michael J. Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA; (M.J.N.); (S.A.)
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA; (M.J.N.); (S.A.)
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA;
- Correspondence: ; Tel.: +402-472-3510; Fax: +402-472-4474
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Jia S, Yobi A, Naldrett MJ, Alvarez S, Angelovici R, Zhang C, Holding DR. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. J Exp Bot 2020; 71:5880-5895. [PMID: 32667993 DOI: 10.1093/jxb/eraa325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Opaque kernels in maize may result from mutations in many genes, such as OPAQUE-2. In this study, a maize null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4) showed an opaque kernel phenotype, as well as plant developmental delay, male sterility, and altered response to cold stress. We found that in opaque kernels, all zein proteins were reduced and amino acid content was changed, including increased lysine. Transcriptomic and proteomic analysis confirmed the zein reduction and proteomic rebalancing of non-zein proteins, which was quantitatively and qualitatively different from opaque-2. Global transcriptional changes were found in endosperm and leaf, including many transcription factors and tissue-specific expressed genes. Furthermore, of the more than 8000 significantly differentially expressed genes in wild type in response to cold, a significant proportion (25.9% in moderate cold stress and 40.8% in near freezing stress) were not differentially expressed in response to cold in rdm4, suggesting RDM4 may participate in regulation of abiotic stress tolerance. This initial characterization of maize RDM4 provides a basis for further investigating its function in endosperm and leaf, and as a regulator of normal and stress-responsive development.
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Affiliation(s)
- Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Pratacultural Science, Beijing Municipality, Beijing, China
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - Abou Yobi
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ruthie Angelovici
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - David R Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
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Guha S, Paul C, Alvarez S, Mine Y, Majumder K. Dietary γ-Glutamyl Valine Ameliorates TNF-α-Induced Vascular Inflammation via Endothelial Calcium-Sensing Receptors. J Agric Food Chem 2020; 68:9139-9149. [PMID: 32786865 PMCID: PMC8012099 DOI: 10.1021/acs.jafc.0c04526] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
γ-Glutamyl valine (γ-EV), commonly found in edible beans, was shown to reduce gastrointestinal inflammation via activation of calcium-sensing receptors (CaSRs). The present study aimed to evaluate the efficacy of γ-EV in modulating the tumor necrosis factor-α-induced inflammatory responses in endothelial cells (ECs) via CaSR-mediated pathways. Human aortic ECs (HAoECs) were pretreated (2 h) with γ-EV (0.01, 0.1, and 1 mM). 1 mM pretreatment of γ-EV significantly reduced the upregulation of inflammatory adhesion molecules, VCAM-1 and E-selectin, by 44.56 and 57.41%, respectively. The production of cytokines IL-8 and IL-6 was significantly reduced by 40 and 51%, respectively, with 1 mM pretreatment of γ-EV. Similarly, there was a significant reduction in chemokine MCP-1 from a positive control of 9.70 ± 0.52 to 6.6 ± 0.43 ng/mL, after γ-EV treatment. The anti-inflammatory effect of γ-EV was attenuated by the treatment of the CaSR-specific inhibitor, NPS-2143, suggesting the involvement of CaSR-mediated pathways. Further studies identified the critical role of key modulators, such as β-arrestin2 and cyclic adenosine monophosphate response element-binding protein, in mediating the CaSR-dependent anti-inflammatory effect of γ-EV. Finally, the transport efficiency of γ-EV was evaluated through a monolayer of intestinal epithelial cells (Caco-2), and the apparent permeability (Papp) of the peptide was found to be 1.56 × 10-6 cm/s.
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Affiliation(s)
- Snigdha Guha
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588, Nebraska, United States
| | - Catherine Paul
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588, Nebraska, United States
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln 68588, Nebraska, United States
| | - Yoshinori Mine
- Department of Food Science, University of Guelph, Guelph N1G2W1, Ontario, Canada
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588, Nebraska, United States
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Edwards RL, Heueck I, Lee SG, Shah IT, Miller JJ, Jezewski AJ, Mikati MO, Wang X, Brothers RC, Heidel KM, Osbourn DM, Burnham CAD, Alvarez S, Fritz SA, Dowd CS, Jez JM, Odom John AR. Potent, specific MEPicides for treatment of zoonotic staphylococci. PLoS Pathog 2020; 16:e1007806. [PMID: 32497104 PMCID: PMC7297381 DOI: 10.1371/journal.ppat.1007806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/16/2020] [Accepted: 04/11/2020] [Indexed: 12/20/2022] Open
Abstract
Coagulase-positive staphylococci, which frequently colonize the mucosal surfaces of animals, also cause a spectrum of opportunistic infections including skin and soft tissue infections, urinary tract infections, pneumonia, and bacteremia. However, recent advances in bacterial identification have revealed that these common veterinary pathogens are in fact zoonoses that cause serious infections in human patients. The global spread of multidrug-resistant zoonotic staphylococci, in particular the emergence of methicillin-resistant organisms, is now a serious threat to both animal and human welfare. Accordingly, new therapeutic targets that can be exploited to combat staphylococcal infections are urgently needed. Enzymes of the methylerythritol phosphate pathway (MEP) of isoprenoid biosynthesis represent potential targets for treating zoonotic staphylococci. Here we demonstrate that fosmidomycin (FSM) inhibits the first step of the isoprenoid biosynthetic pathway catalyzed by deoxyxylulose phosphate reductoisomerase (DXR) in staphylococci. In addition, we have both enzymatically and structurally determined the mechanism by which FSM elicits its effect. Using a forward genetic screen, the glycerol-3-phosphate transporter GlpT that facilitates FSM uptake was identified in two zoonotic staphylococci, Staphylococcus schleiferi and Staphylococcus pseudintermedius. A series of lipophilic ester prodrugs (termed MEPicides) structurally related to FSM were synthesized, and data indicate that the presence of the prodrug moiety not only substantially increased potency of the inhibitors against staphylococci but also bypassed the need for GlpT-mediated cellular transport. Collectively, our data indicate that the prodrug MEPicides selectively and robustly inhibit DXR in zoonotic staphylococci, and further, that DXR represents a promising, druggable target for future development.
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Affiliation(s)
- Rachel L. Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Isabel Heueck
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Soon Goo Lee
- University of North Carolina-Wilmington, Wilmington, North Carolina, United States of America
| | - Ishaan T. Shah
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Justin J. Miller
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew J. Jezewski
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Marwa O. Mikati
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xu Wang
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Robert C. Brothers
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Kenneth M. Heidel
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Damon M. Osbourn
- Department of Chemistry, Saint Louis University, St. Louis, Missouri, United States of America
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Stephanie A. Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States of America
| | - Joseph M. Jez
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Audrey R. Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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33
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Alvarez S, Martinez-Fernandez A, Mendez P. Ensiling potential of fresh tomato waste with dehydrated beet pulp and cereal straw as additives. ANIM NUTR FEED TECHN 2020. [DOI: 10.5958/0974-181x.2020.00034.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, Jez JM. Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid. J Biol Chem 2019; 294:16855-16864. [PMID: 31575658 DOI: 10.1074/jbc.ra119.009949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/29/2019] [Indexed: 11/06/2022] Open
Abstract
To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. The model plant Arabidopsis thaliana has 19 GH3 proteins, of which 8 have confirmed biochemical functions. One Brassicaceae-specific clade of GH3 proteins was predicted to use benzoate as a substrate and includes AtGH3.7 and AtGH3.12/PBS3. Previously identified as a 4-hydroxybenzoic acid-glutamate synthetase, AtGH3.12/PBS3 influences pathogen defense responses through salicylic acid. Recent work has shown that AtGH3.12/PBS3 uses isochorismate as a substrate, forming an isochorismate-glutamate conjugate that converts into salicylic acid. Here, we show that AtGH3.7 and AtGH3.12/PBS3 can also conjugate chorismate to cysteine and glutamate, which act as precursors to aromatic amino acids and salicylic acid, respectively. The X-ray crystal structure of AtGH3.12/PBS3 in complex with AMP and chorismate at 1.94 Å resolution, along with site-directed mutagenesis, revealed how the active site potentially accommodates this substrate. Examination of Arabidopsis knockout lines indicated that the gh3.7 mutants do not alter growth and showed no increased susceptibility to the pathogen Pseudomonas syringae, unlike gh3.12 mutants, which were more susceptible than WT plants, as was the gh3.7/gh3.12 double mutant. The findings of our study suggest that GH3 proteins can use metabolic precursors of aromatic amino acids as substrates.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jason E Schaffer
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, University Grenoble Alpes, CNRS, CEA, INRA, IRIG, Grenoble, France
| | - Sophie Alvarez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130
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35
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Qian PC, Barry MA, Lu J, Pouliopoulos J, Mina A, Bandodkar S, Alvarez S, James V, Ronquillo J, Varikatt W, Thiagalingam A, Thomas S. 1196Transvascular pace-capture of aorticorenal ganglia provides a testable procedural endpoint for transcatheter renal artery denervation and identifies a novel therapeutic ablation target for denervation. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Transcatheter renal denervation procedures often produces incomplete renal denervation and inconsistent antihypertensive effect. The lack of an intraprocedural method for renal sympathetic nerve function assessment has precluded a rational and physiologically based approach to ensure adequate denervation has been achieved at the time of the procedure.
Purpose
To demonstrate that it is possible to localise aorticorenal ganglia via transvascular pacing to provide: 1) a testable procedural endpoint for transcatheter renal denervation and, 2) a novel ablation target for renal denervation.
Methods
High frequency pacing in the inferior vena cava and aorta, invasive blood pressure measurements and renal angiography was performed in sheep (N=19) to identify ARG pace-capture sites by concurrent hypertensive and renal vasoconstrictive responses. Group A (N=5) underwent ink injection labelling at the ARG pace-capture site for histological verification; Group B (N=6) received unilateral irrigated radiofrequency ablation of ARG pace-capture sites and assessment of renal innervation at 1week post-procedure; and Group C (N=8) had ARG pacing performed prior to and 2–3 weeks after unilateral transcatheter microwave renal denervation.
Results
ARG pace-capture responses were observed at paired discrete sites in the posterior IVC and anterolateral aorta approximately 40mm above the ipsilateral renal artery. Pacing elicited a mean arterial blood pressure change of 22.2 [IQR 15.5–34.3] mmHg, p<0.001, together with ipsilateral renal vasoconstriction with main renal artery calibre change of −0.42mm [IQR −0.64mm to −0.24mm] measured with quantitative coronary analysis (QCA), p<0.0001, and branch renal artery median pixel density index change −10.4% [IQR −22.7% to −3.0%], p=0.003. Contralateral renal arterial vasoconstriction was not observed consistently at either the main or branch renal artery level. Sympathetic ganglionic tissue was observed at ARG pace-capture sites, and ganglion ablation caused significant ipsilateral renal denervation with a median hilar functional sympathetic nerve area reduction of 51% [IQR 24%–52%], p=0.043, and renal cortical norepinephrine reduction of 54% [IQR 36%–59%], p=0.043. Circumferential renal denervation resulted in immediate and sustained abolition of ARP pacing induced renal vasoconstriction and significant ipsilateral renal denervation.
Conclusion
Localisation of ARG using transvascular pacing is feasible with pace-capture demonstrated by concurrent hypertensive and ipsilateral renal arterial vasoconstrictive responses. Abolition of ARG pacing induced renal arterial vasoconstriction may indicate successful renal sympathetic denervation, providing a physiological procedural endpoint to guide transcatheter renal denervation. Additionally, ablation of ARG could provide an alternative or adjunctive method for renal denervation.
Acknowledgement/Funding
University of Sydney; Western Sydney Local health District; National Health and Medical Research Council of Australia; National Heart Foundation (Au)
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Affiliation(s)
- P C Qian
- Westmead Hospital, Cardiology, Sydney, Australia
| | - M A Barry
- Westmead Hospital, Cardiology, Sydney, Australia
| | - J Lu
- Westmead Hospital, Cardiology, Sydney, Australia
| | | | - A Mina
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - S Bandodkar
- The Children's Hospital at Westmead, Biochemistry, Sydney, Australia
| | - S Alvarez
- The Children's Hospital at Westmead, Biochemistry, Sydney, Australia
| | - V James
- Westmead Institute for Medical Research, Histology, Sydney, Australia
| | - J Ronquillo
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - W Varikatt
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | | | - S Thomas
- Westmead Hospital, Cardiology, Sydney, Australia
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Qian P, Barry MA, Lu J, Mina A, Ryan J, Bandodkar S, Alvarez S, James V, Ronquillo J, Varikatt W, Kovoor P, Pouliopoulos J, McEwan A, Thiagalingam A, Thomas S. 1197The development and validation of a novel transcatheter microwave renal denervation system. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Clinical studies of transcatheter radiofrequency renal denervation for treating hypertension have been hampered by the lack of consistent denervation efficacy. Microwave energy is well suited to renal denervation due to its capacity to spare vascular structures due to cooling from adjacent blood flow while enabling deep perivascular heating.
Purpose
We aimed to: 1) develop a transcatheter microwave system capable of safely delivering deep and circumferential perivascular renal nerve ablation, and 2) demonstrate the feasibility, short-term efficacy and safety of transcatheter microwave renal denervation.
Method
A novel 7F transcatheter microwave denervation system was designed, built, and iteratively prototyped in vitro and in 15 sheep. A histological grading system for microwave induced renal arterial and renal nerve injury was devised. The microwave denervation system was validated in an additional 9 sheep, which underwent unilateral renal denervation. Up to 2 microwave ablations were delivered to each artery with maximum power at 100–110W for 480s. Sheep were euthanised at 2–3 weeks post procedure. Gross microscopic histological examination as well as renal tissue norepinephrine content was analysed.
Results
Catheter deployment and ablation was successful in all 19 targeted vessel segments and ablation produced substantial circumferential perivascular injury; median ablation lesion area >395 (IQR 251–437) mm2, depth 17.1 (IQR 15.8–18.4) mm, length 16 (IQR 12–20) mm, without collateral visceral injury. Limiting power to 100W minimised arterial injury, while maintaining a deep circumferential perivascular ablation. At microwave ablation sites, a total of 292 nerve fascicles were identified, median distance from the renal artery of 4.2mm (IQR 2.1–8.8mm), of which 249 (85%) had sustained thermal injury with 128/249 (51%) showing grade 3–4 (moderate to severe) injury. Microwave denervation reduced median functional sympathetic nerve surface area at the renal hilum on anti-tyrosine hydroxylase staining by 100% (IQR 87%-100%), p=0.0039, and median renal cortical norepinephrine content by 83% (IQR 76%–92%), p=0.0078, compared to the paired control kidney.
Conclusion
Transcatheter microwave ablation can produce deep circumferential perivascular ablations over a long segment of the renal artery without significant arterial or collateral visceral injury to provide effective renal denervation. Clinical translation may enable more consistent and complete transcatheter renal denervation and antihypertensive efficacy.
Acknowledgement/Funding
University of Sydney; Western Sydney Local health District; National Health and Medical Research Council of Australia; National Heart Foundation (Au)
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Affiliation(s)
- P Qian
- Westmead Hospital, Sydney, Australia
| | - M A Barry
- Westmead Hospital, Cardiology, Sydney, Australia
| | - J Lu
- Westmead Hospital, Cardiology, Sydney, Australia
| | - A Mina
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - J Ryan
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - S Bandodkar
- The Children's Hospital at Westmead, Biochemistry, Sydney, Australia
| | - S Alvarez
- The Children's Hospital at Westmead, Biochemistry, Sydney, Australia
| | - V James
- Westmead Institute for Medical Research, Histology, Sydney, Australia
| | - J Ronquillo
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - W Varikatt
- Westmead Hospital, Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - P Kovoor
- Westmead Hospital, Cardiology, Sydney, Australia
| | | | - A McEwan
- Westmead Hospital, Sydney, Australia
| | | | - S Thomas
- Westmead Hospital, Sydney, Australia
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Comer JD, Alvarez S, Butler SJ, Kaltschmidt JA. Commissural axon guidance in the developing spinal cord: from Cajal to the present day. Neural Dev 2019; 14:9. [PMID: 31514748 PMCID: PMC6739980 DOI: 10.1186/s13064-019-0133-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
During neuronal development, the formation of neural circuits requires developing axons to traverse a diverse cellular and molecular environment to establish synaptic contacts with the appropriate postsynaptic partners. Essential to this process is the ability of developing axons to navigate guidance molecules presented by specialized populations of cells. These cells partition the distance traveled by growing axons into shorter intervals by serving as intermediate targets, orchestrating the arrival and departure of axons by providing attractive and repulsive guidance cues. The floor plate in the central nervous system (CNS) is a critical intermediate target during neuronal development, required for the extension of commissural axons across the ventral midline. In this review, we begin by giving a historical overview of the ventral commissure and the evolutionary purpose of decussation. We then review the axon guidance studies that have revealed a diverse assortment of midline guidance cues, as well as genetic and molecular regulatory mechanisms required for coordinating the commissural axon response to these cues. Finally, we examine the contribution of dysfunctional axon guidance to neurological diseases.
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Affiliation(s)
- J D Comer
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.,Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - S Alvarez
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - S J Butler
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - J A Kaltschmidt
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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38
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Lagundžin D, Hu WF, Law HCH, Krieger KL, Qiao F, Clement EJ, Drincic AT, Nedić O, Naldrett MJ, Alvarez S, Woods NT. Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactome. PLoS One 2019; 14:e0220568. [PMID: 31461451 PMCID: PMC6713327 DOI: 10.1371/journal.pone.0220568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
Hyperinsulinemia affects 72% of Fanconi anemia (FA) patients and an additional 25% experience lowered glucose tolerance or frank diabetes. The underlying molecular mechanisms contributing to the dysfunction of FA pancreas β cells is unknown. Therefore, we sought to evaluate the functional role of FANCA, the most commonly mutated gene in FA, in glucose-stimulated insulin secretion (GSIS). This study reveals that FANCA or FANCB knockdown impairs GSIS in human pancreas β cell line EndoC-βH3. To identify potential pathways by which FANCA might regulate GSIS, we employed a proteomics approach to identify FANCA protein interactions in EndoC-βH3 differentially regulated in response to elevated glucose levels. Glucose-dependent changes in the FANCA interaction network were observed, including increased association with other FA family proteins, suggesting an activation of the DNA damage response in response to elevated glucose levels. Reactive oxygen species increase in response to glucose stimulation and are necessary for GSIS in EndoC-βH3 cells. Glucose-induced activation of the DNA damage response was also observed as an increase in the DNA damage foci marker γ-H2AX and dependent upon the presence of reactive oxygen species. These results illuminate the role of FANCA in GSIS and its protein interactions regulated by glucose stimulation that may explain the prevalence of β cell-specific endocrinopathies in FA patients.
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Affiliation(s)
- Dragana Lagundžin
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Wen-Feng Hu
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Henry C. H. Law
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kimiko L. Krieger
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Fangfang Qiao
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Emalie J. Clement
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Andjela T. Drincic
- Department of Internal Medicine: Diabetes, Endocrinology and Metabolism, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy, University of Belgrade, Banatska, Belgrade, Serbia
| | - Michael J. Naldrett
- Proteomics & Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska–Lincoln, Nebraska, United States of America
| | - Sophie Alvarez
- Proteomics & Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska–Lincoln, Nebraska, United States of America
| | - Nicholas T. Woods
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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39
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Shihabudeen Haider Ali MS, Cheng X, Moran M, Haemmig S, Naldrett MJ, Alvarez S, Feinberg MW, Sun X. LncRNA Meg3 protects endothelial function by regulating the DNA damage response. Nucleic Acids Res 2019; 47:1505-1522. [PMID: 30476192 PMCID: PMC6379667 DOI: 10.1093/nar/gky1190] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 01/10/2023] Open
Abstract
The role of long non-coding RNAs (lncRNAs) in regulating endothelial function through the DNA damage response (DDR) remains poorly understood. In this study, we demonstrate that lncRNA maternally expressed gene 3 (Meg3) interacts with the RNA binding protein polypyrimidine tract binding protein 3 (PTBP3) to regulate gene expression and endothelial function through p53 signaling ─ a major coordinator of apoptosis and cell proliferation triggered by the DDR. Meg3 expression is induced in endothelial cells (ECs) upon p53 activation. Meg3 silencing induces DNA damage, activates p53 signaling, increases the expression of p53 target genes, promotes EC apoptosis, and inhibits EC proliferation. Mechanistically, Meg3 silencing reduces the interaction of p53 with Mdm2, induces p53 expression, and promotes the association of p53 with the promoters of a subset of p53 target genes. PTBP3 silencing recapitulates the effects of Meg3 deficiency on the expression of p53 target genes, EC apoptosis and proliferation. The Meg3-dependent association of PTBP3 with the promoters of p53 target genes suggests that Meg3 and PTBP3 restrain p53 activation. Our studies reveal a novel role of Meg3 and PTBP3 in regulating p53 signaling and endothelial function, which may serve as novel targets for therapies to restore endothelial homeostasis.
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Affiliation(s)
| | - Xiao Cheng
- Department of Biochemistry, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Matthew Moran
- Department of Biochemistry, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Stefan Haemmig
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Center for Biotechnology, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Center for Biotechnology, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE 68588, USA
- Nebraska Center for the Prevention of Obesity Diseases through Dietary Molecules, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Lin L, Tham E, Islam S, Alvarez S, Mah K, Colen T, Kutty S, Joseph N, Li L, Khoo N. HYPOPLASTIC LEFT HEART SYNDROME SPECK TRACKING ECHOCARDIOGRAPHY ATRIAL CONDUIT STRAIN AND STRAIN RATE IS RELATED TO VENTRICULAR DIASTOLIC CHANGES: A LONGITUDINAL STUDY. Can J Cardiol 2018. [DOI: 10.1016/j.cjca.2018.07.327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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41
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Bizimungu R, Alvarez S, Rodriguez R. 290 Thoracic Spine Fracture in the Pan Scan Era. Ann Emerg Med 2018. [DOI: 10.1016/j.annemergmed.2018.08.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Lin L, Tham E, Islam S, Alvarez S, Mah K, Colen T, Kutty S, Joseph N, Li L, Khoo N. INCREASED PRELOAD AND AFTERLOAD STRESSORS DURING THE FIRST INTERSTAGE MAY UNMASK IMPAIRED RIGHT VENTRICULAR CONTRACTILE RESERVE IN HYPOPLASTIC LEFT HEART SYNDROME (HLHS): A LONGITUDINAL SPECKLE TRACKING ECHOCARDIOGRAPHY STUDY. Can J Cardiol 2018. [DOI: 10.1016/j.cjca.2018.07.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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43
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Wang X, Edwards RL, Ball H, Johnson C, Haymond A, Girma M, Manikkam M, Brothers RC, McKay KT, Arnett SD, Osbourn DM, Alvarez S, Boshoff HI, Meyers MJ, Couch RD, Odom John AR, Dowd CS. MEPicides: α,β-Unsaturated Fosmidomycin Analogues as DXR Inhibitors against Malaria. J Med Chem 2018; 61:8847-8858. [PMID: 30192536 DOI: 10.1021/acs.jmedchem.8b01026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Severe malaria due to Plasmodium falciparum remains a significant global health threat. DXR, the second enzyme in the MEP pathway, plays an important role to synthesize building blocks for isoprenoids. This enzyme is a promising drug target for malaria due to its essentiality as well as its absence in humans. In this study, we designed and synthesized a series of α,β-unsaturated analogues of fosmidomycin, a natural product that inhibits DXR in P. falciparum. All compounds were evaluated as inhibitors of P. falciparum. The most promising compound, 18a, displays on-target, potent inhibition against the growth of P. falciparum (IC50 = 13 nM) without significant inhibition of HepG2 cells (IC50 > 50 μM). 18a was also tested in a luciferase-based Plasmodium berghei mouse model of malaria and showed exceptional in vivo efficacy. Together, the data support MEPicide 18a as a novel, potent, and promising drug candidate for the treatment of malaria.
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Affiliation(s)
- Xu Wang
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| | - Rachel L Edwards
- Department of Pediatrics , Washington University School of Medicine, Washington University , St. Louis , Missouri 63110 , United States
| | - Haley Ball
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Claire Johnson
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Amanda Haymond
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Misgina Girma
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Michelle Manikkam
- Tuberculosis Research Section, LCIM , NIAID/NIH , Bethesda , Maryland 20892 , United States
| | - Robert C Brothers
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| | - Kyle T McKay
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| | - Stacy D Arnett
- Department of Pharmacology and Physiology , Saint Louis University , St. Louis , Missouri 63104 , United States
| | - Damon M Osbourn
- Department of Molecular Microbiology and Immunology , Saint Louis University , St. Louis , Missouri 63104 , United States
| | - Sophie Alvarez
- Proteomics & Metabolomics Facility, Center for Biotechnology, Department of Agronomy and Horticulture , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Helena I Boshoff
- Tuberculosis Research Section, LCIM , NIAID/NIH , Bethesda , Maryland 20892 , United States
| | - Marvin J Meyers
- Department of Pharmacology and Physiology , Saint Louis University , St. Louis , Missouri 63104 , United States.,Department of Chemistry , Saint Louis University , St. Louis , Missouri 63103 , United States
| | - Robin D Couch
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Audrey R Odom John
- Department of Pediatrics , Washington University School of Medicine, Washington University , St. Louis , Missouri 63110 , United States
| | - Cynthia S Dowd
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
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Reid G, Kort R, Alvarez S, Bourdet-Sicard R, Benoit V, Cunningham M, Saulnier D, van Hylckama Vlieg J, Verstraelen H, Sybesma W. Expanding the reach of probiotics through social enterprises. Benef Microbes 2018; 9:707-715. [DOI: 10.3920/bm2018.0015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The rapid rise in microbiome and probiotic science has led to estimates of product creation and sales exceeding $50 billion within five years. However, many people do not have access to affordable products, and regulatory agencies have stifled progress. The objective of a discussion group at the 2017 meeting of the International Scientific Association for Probiotics and Prebiotics was to identify mechanisms to confer the benefits of probiotics to a larger portion of the world’s population. Three initiatives, built around fermented food, were discussed with different methods of targeting populations that face enormous challenges of malnutrition, infectious disease, poverty and violent conflict. As new candidate probiotic strains emerge, and the market diversifies towards more personalised interventions, manufacturing processes will need to evolve. Information dissemination through scientific channels and social media is projected to provide consumers and healthcare providers with rapid access to clinical results, and to identify the nearest location of sites making new and affordable probiotic food and supplements. This rapid translation of science to individual well-being will not only expand the beneficiaries of probiotics, but also fuel new social enterprises and economic business models.
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Affiliation(s)
- G. Reid
- Canadian Research and Development Centre for Probiotics, Microbiology & Immunology, and Surgery, University of Western Ontario, Room F3-106, P.O. Box 5777, STN B, London, N6A 4V2 Ontario, Canada
| | - R. Kort
- Yoba for Life foundation, Hunzestraat 133-A, 1079 WB Amsterdam, the Netherlands
- TNO Microbiology and Systems Biology, P.O. Box 360, 3700 AJ Zeist, the Netherlands
- VU University Amsterdam; Micropia, Natura Artis Magistra, Plantage Kerklaan 38-40, 1018 CZ Amsterdam, the Netherlands
| | - S. Alvarez
- Reference Centre for Lactobacilli (CERELA-CONICET), Chacabuco 145, Tucuman 4000, Argentina
| | - R. Bourdet-Sicard
- Danone Access, Africa & India, Danone Nutricia Research, Avenue de la Vauve, 91767 Palaiseau, France
| | - V. Benoit
- General Mills, Nutrition and Technology Solutions, 9000 Plymouth Avenue N, Minneapolis, MN 55427, USA
| | - M. Cunningham
- Research and Development, Metagenics (Aust) Pty Ltd., P.O. Box 675, Virginia BC, Queensland 4014, Australia
| | - D.M. Saulnier
- Novozymes A/S, Hillerødgade 42, 2200 Frederiksberg, Denmark
| | | | - H. Verstraelen
- Vulvovaginal Disease Clinic, Dept. of Obstetrics & Gynaecology, Ghent University Hospital 0P4, Corneel Heymanslaan 10, 9000 Gent, Belgium
| | - W. Sybesma
- Yoba for Life foundation, Hunzestraat 133-A, 1079 WB Amsterdam, the Netherlands
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Clement A, Cornet D, Alvarez S, Brami C, Clement P, Menezo Y. Endometriosis pathogenesis : role played by the oxidative stress due to MTHFR mutations. Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Perdigón G, Alvarez S, Medina M, Vintini E, Roux E. Influence of the Oral Administration of Lactic Acid Bacteria on Iga Producing Cells Associated to Bronchus. Int J Immunopathol Pharmacol 2018. [DOI: 10.1177/205873929901200207] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- G. Perdigón
- Centro de Referencia para Lactobacilos (CERELA). Chacabuco 145. 4000. Tucumcín. Argentina
- C-tedra de Inmunologia. Instituto de Microbiologia. Facultad de Bioquimica, Quimica y Farmacia de la Universidad Nacional de Tucumcín
| | - S. Alvarez
- Centro de Referencia para Lactobacilos (CERELA). Chacabuco 145. 4000. Tucumcín. Argentina
- C-tedra de Inmunologia. Instituto de Microbiologia. Facultad de Bioquimica, Quimica y Farmacia de la Universidad Nacional de Tucumcín
| | - M. Medina
- Centro de Referencia para Lactobacilos (CERELA). Chacabuco 145. 4000. Tucumcín. Argentina
| | - E. Vintini
- C-tedra de Inmunologia. Instituto de Microbiologia. Facultad de Bioquimica, Quimica y Farmacia de la Universidad Nacional de Tucumcín
| | - E. Roux
- Laboratorio de Inmunologia Celular. Facultad de Farmacia y Bioquimica, Universidad Nacional de Buenos Aires
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Cobos M, Aquilia L, Garay E, Ochiuzzi S, Alvarez S, Flores D, Raimondi C. Epidemiologic Study and Genotyping of BK Virus in Renal Transplant Recipients. Transplant Proc 2018; 50:458-460. [DOI: 10.1016/j.transproceed.2017.12.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/05/2017] [Indexed: 10/17/2022]
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Sherp AM, Westfall CS, Alvarez S, Jez JM. Arabidopsis thaliana GH3.15 acyl acid amido synthetase has a highly specific substrate preference for the auxin precursor indole-3-butyric acid. J Biol Chem 2018; 293:4277-4288. [PMID: 29462792 DOI: 10.1074/jbc.ra118.002006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
Various phytohormones control plant growth and development and mediate biotic and abiotic stress responses. Gretchen Hagen 3 (GH3) acyl acid amido synthetases are plant enzymes that typically conjugate amino acids to indole-3-acetic acid (IAA) or jasmonic acid (JA) to inactivate or activate these phytohormones, respectively; however, the physiological and biological roles of many of these enzymes remain unclear. Using a biochemical approach, we found that the Arabidopsis thaliana GH3.15 (AtGH3.15) preferentially uses indole-3-butyric acid (IBA) and glutamine as substrates. The X-ray crystal structure of the AtGH3.15·AMP complex, modeling of IBA in the active site, and biochemical analysis of site-directed mutants provide insight on active site features that lead to AtGH3.15's preference for IBA. Assay-based in planta analysis of AtGH3.15-overexpressing lines indicated that their root elongation and lateral root density were resistant to IBA treatment but not to treatment with either IAA or JA. These findings suggest that AtGH3.15 may play a role in auxin homeostasis by modulating the levels of IBA for peroxisomal conversion to IAA. Analysis of AtGH3.15 promoter-driven yellow fluorescent protein reporter lines revealed that AtGH3.15 is expressed at significant levels in seedlings, roots, and parts of the siliques. We conclude that AtGH3.15 is unique in the GH3 protein family for its role in modifying IBA in auxin homeostasis and that it is the first GH3 protein shown to primarily modify a plant growth regulator other than IAA and JA.
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Affiliation(s)
- Ashley M Sherp
- From the Department of Biology, Washington University, St. Louis, Missouri 63130 and
| | - Corey S Westfall
- From the Department of Biology, Washington University, St. Louis, Missouri 63130 and
| | - Sophie Alvarez
- the Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130 and
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Qian P, Barry M, Lu J, Al-Raisi S, Mina A, Ryan J, Bandodkar S, Alvarez S, James V, Ronquillo J, Varikatt W, Clayton Z, Chong J, Kovoor P, Pouliopoulos J, McEwan A, Thiagalingam A, Thomas S. Development and Validation of a Novel Microwave Transcatheter Renal Denervation System and an Intraprocedural Physiological End Point for Renal Sympathetic Denervation. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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50
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Huang H, Gehan MA, Huss SE, Alvarez S, Lizarraga C, Gruebbling EL, Gierer J, Naldrett MJ, Bindbeutel RK, Evans BS, Mockler TC, Nusinow DA. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. Plant Direct 2017; 1:e00018. [PMID: 31245666 PMCID: PMC6508535 DOI: 10.1002/pld3.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 09/13/2017] [Indexed: 05/03/2023]
Abstract
Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana (Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside of Arabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function of Brachypodium distachyon (Brachypodium) and Setaria viridis (Setaria) orthologs of EARLY FLOWERING 3, a key clock gene in Arabidopsis. To identify both cycling genes and putative ELF3 functional orthologs in Setaria, a circadian RNA-seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles of Setaria genes under circadian conditions. The function of ELF3 orthologs from Arabidopsis, Brachypodium, and Setaria was tested for complementation of an elf3 mutation in Arabidopsis. We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF3 and SvELF3 could be integrated into similar complexes in vivo as AtELF3. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Sophie Alvarez
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
| | | | | | - John Gierer
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Michael J. Naldrett
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
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