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Fischer N, Costa CP, Hur M, Kirkwood JS, Woodard SH. Impacts of neonicotinoid insecticides on bumble bee energy metabolism are revealed under nectar starvation. Sci Total Environ 2024; 912:169388. [PMID: 38104805 DOI: 10.1016/j.scitotenv.2023.169388] [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] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Bumble bees are an important group of insects that provide essential pollination services as a consequence of their foraging behaviors. These pollination services are driven, in part, by energetic exchanges between flowering plants and individual bees. Thus, it is important to examine bumble bee energy metabolism and explore how it might be influenced by external stressors contributing to declines in global pollinator populations. Two stressors that are commonly encountered by bees are insecticides, such as the neonicotinoids, and nutritional stress, resulting from deficits in pollen and nectar availability. Our study uses a metabolomic approach to examine the effects of neonicotinoid insecticide exposure on bumble bee metabolism, both alone and in combination with nutritional stress. We hypothesized that exposure to imidacloprid disrupts bumble bee energy metabolism, leading to changes in key metabolites involved in central carbon metabolism. We tested this by exposing Bombus impatiens workers to imidacloprid according to one of three exposure paradigms designed to explore how chronic versus more acute (early or late) imidacloprid exposure influences energy metabolite levels, then also subjecting them to artificial nectar starvation. The strongest effects of imidacloprid were observed when bees also experienced nectar starvation, suggesting a combinatorial effect of neonicotinoids and nutritional stress on bumble bee energy metabolism. Overall, this study provides important insights into the mechanisms underlying the impact of neonicotinoid insecticides on pollinators, and underscores the need for further investigation into the complex interactions between environmental stressors and energy metabolism.
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Affiliation(s)
- Natalie Fischer
- Department of Entomology, University of California, Riverside, Riverside, CA, USA.
| | - Claudinéia P Costa
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Manhoi Hur
- IIGB Metabolomics Core Facility, University of California, Riverside, Riverside, CA, USA
| | - Jay S Kirkwood
- IIGB Metabolomics Core Facility, University of California, Riverside, Riverside, CA, USA
| | - S Hollis Woodard
- Department of Entomology, University of California, Riverside, Riverside, CA, USA.
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2
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Nye DG, Irigoyen ML, Perez-Fons L, Bohorquez-Chaux A, Hur M, Medina-Yerena D, Lopez-Lavalle LAB, Fraser PD, Walling LL. Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance. BMC Plant Biol 2023; 23:657. [PMID: 38124051 PMCID: PMC10731783 DOI: 10.1186/s12870-023-04607-y] [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] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Whiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated. RESULTS Whitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246's response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava's hormone-responsive genes showed striking divergence in expression. CONCLUSIONS This study provides the first characterization of cassava's global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.
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Affiliation(s)
- Danielle G Nye
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Maria L Irigoyen
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Laura Perez-Fons
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Adriana Bohorquez-Chaux
- Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Manhoi Hur
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Diana Medina-Yerena
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Luis Augusto Becerra Lopez-Lavalle
- Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Present Address: International Center of Biosaline Agriculture, Dubai, United Arab Emirates
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
- Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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Choi HS, Bjornson M, Liang J, Wang J, Ke H, Hur M, De Souza A, Kumar KS, Mortimer JC, Dehesh K. COG-imposed Golgi functional integrity determines the onset of dark-induced senescence. Nat Plants 2023; 9:1890-1901. [PMID: 37884654 DOI: 10.1038/s41477-023-01545-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023]
Abstract
Plant survival depends on dynamic stress-response pathways in changing environments. To uncover pathway components, we screened an ethyl methanesulfonate-mutagenized transgenic line containing a stress-inducible luciferase construct and isolated a constitutive expression mutant. The mutant is the result of an amino acid substitution in the seventh subunit of the hetero-octameric conserved oligomeric Golgi (COG) complex of Arabidopsis thaliana. Complementation studies verified the Golgi localization of cog7, and stress tests established accelerated dark-induced carbon deprivation/senescence of the mutant compared with wild-type plants. Multiomics and biochemical analyses revealed accelerated induction of protein ubiquitination and autophagy, and a counterintuitive increased protein N-glycosylation in senescencing cog7 relative to wild-type. A revertant screen using the overexpressor (FOX)-hunting system established partial, but notable rescue of cog7 phenotypes by COG5 overexpression, and conversely premature senescence in reduced COG5 expressing lines. These findings identify COG-imposed Golgi functional integrity as a main player in ensuring cellular survival under energy-limiting conditions.
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Affiliation(s)
- Hee-Seung Choi
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Marta Bjornson
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jiubo Liang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Jinzheng Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Manhoi Hur
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Amancio De Souza
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | | | - Jenny C Mortimer
- Lawrence Berkeley National Lab, Joint BioEnergy Institute, Emeryville, CA, USA
- School of Agriculture Food and Wine & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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Pervaiz T, Park S, Rezk A, Hur M, Obenland D, Arpaia ML, El-kereamy A. Metabolomic analyses provide insights into the preharvest rind disorder in Satsuma Owari Mandarin. Front Plant Sci 2023; 14:1263354. [PMID: 37822340 PMCID: PMC10562707 DOI: 10.3389/fpls.2023.1263354] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 10/13/2023]
Abstract
Citrus fruit's appearance is the primary criterion used to assess its quality for the fresh market, hence the rind's condition is a crucial quality trait. Pre-harvest rind disorder is one of the major physiological problems in mandarins. The disorder occurs right before harvest following rain events in some Mandarin varieties. Despite the economic damage caused by this kind of disorder, very limited information is available about the molecular mechanisms underlying the occurrence of this disorder. In the present study, we evaluated the primary metabolites, antioxidants, and hormones associated with the pre-harvest rind disorder in Mandarins. The study was carried out using ten-year-old 'Owari' Satsuma mandarin trees grafted on 'Carrizo' rootstock and grown in a commercial orchard in San Joaquin Valley, California, USA. Samples were collected from healthy tissue of healthy fruit (HF_HT), healthy tissue of damaged fruit (DF_HT), and damaged tissue of damaged fruit (DF_DT). Damaged fruit (DF_HT and DF_DT) showed lower cellulose concentrations than healthy fruit tissues (HF_HT), however, had similar contents of pectin and hemicellulose. The antioxidant activities showed no significant difference in all paired comparisons between samples as expressed in the malondialdehyde (MDA) content. However, DF_DT had a higher H2O2 content compared to HF_HT, but DF_HT had a similar content to that of HF_HT. Furthermore, peroxidase (POD) and polyphenol oxidase (PPO) activities were increased in DF_DT compared to HF_HT (P = 0.0294) and DF_HT (P = 0.0044), respectively. Targeted metabolomics analysis revealed that a total of 76 metabolites were identified in Satsuma rind tissues, and the relative concentrations of 43 metabolites were significantly different across studied samples. The hormonal analysis showed the involvement of jasmonate O-methyltransferase, jasmonic acid-amido synthetase JAR1-like, and JA-isoleucine may key role in causing the rind disorder in mandarins. In addition, the damaged fruit tissues have a higher level of jasmonic acid (JA), 12-oxo-phytodienoic acid, and JA-isoleucine than undamaged tissue.
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Affiliation(s)
- Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Suejin Park
- Department of Horticulture, Jeonbuk National University, Jeonju, Republic of Korea
| | - Alaaeldin Rezk
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - David Obenland
- United States Department of Agriculture (USDA), Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Mary Lu Arpaia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Ashraf El-kereamy
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
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Talvio K, Wagner VA, Minkeviciene R, Kirkwood JS, Kulinich AO, Umemori J, Bhatia A, Hur M, Käkelä R, Ethell IM, Castrén ML. An iPSC-derived astrocyte model of fragile X syndrome exhibits dysregulated cholesterol homeostasis. Commun Biol 2023; 6:789. [PMID: 37516746 PMCID: PMC10387075 DOI: 10.1038/s42003-023-05147-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/14/2023] [Indexed: 07/31/2023] Open
Abstract
Cholesterol is an essential membrane structural component and steroid hormone precursor, and is involved in numerous signaling processes. Astrocytes regulate brain cholesterol homeostasis and they supply cholesterol to the needs of neurons. ATP-binding cassette transporter A1 (ABCA1) is the main cholesterol efflux transporter in astrocytes. Here we show dysregulated cholesterol homeostasis in astrocytes generated from human induced pluripotent stem cells (iPSCs) derived from males with fragile X syndrome (FXS), which is the most common cause of inherited intellectual disability. ABCA1 levels are reduced in FXS human and mouse astrocytes when compared with controls. Accumulation of cholesterol associates with increased desmosterol and polyunsaturated phospholipids in the lipidome of FXS mouse astrocytes. Abnormal astrocytic responses to cytokine exposure together with altered anti-inflammatory and cytokine profiles of human FXS astrocyte secretome suggest contribution of inflammatory factors to altered cholesterol homeostasis. Our results demonstrate changes of astrocytic lipid metabolism, which can critically regulate membrane properties and affect cholesterol transport in FXS astrocytes, providing target for therapy in FXS.
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Affiliation(s)
- Karo Talvio
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Victoria A Wagner
- Division of Biomedical Sciences, and Neuroscience Graduate Program, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Rimante Minkeviciene
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Anna O Kulinich
- Division of Biomedical Sciences, and Neuroscience Graduate Program, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Juzoh Umemori
- Gene and Cell Technology, A.I.Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Anil Bhatia
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Reijo Käkelä
- Helsinki University Lipidomics Unit, HiLIPID, Helsinki Institute of Life Science, HiLIFE, Biocenter Finland (Metabolomics), and Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Iryna M Ethell
- Division of Biomedical Sciences, and Neuroscience Graduate Program, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Maija L Castrén
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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Yim WC, Swain ML, Ma D, An H, Bird KA, Curdie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, Cushman JC, Edger PP, Mason AS, Pires JC, Tang H, Zhang X. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. Plant Cell 2022; 34:4143-4172. [PMID: 35961044 PMCID: PMC9614464 DOI: 10.1093/plcell/koac249] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/24/2022] [Indexed: 05/05/2023]
Abstract
Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.
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Affiliation(s)
| | | | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - David D Curdie
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel Wang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hyun Don Ham
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Juan K Q Solomon
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada, Reno, Nevada 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Annaliese S Mason
- Plant Breeding Department, INRES, The University of Bonn, Bonn 53115, Germany
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, , University of Missouri, Columbia, Missouri 65211, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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Costa CP, Leza M, Duennes MA, Fisher K, Vollaro A, Hur M, Kirkwood JS, Woodard SH. Pollen diet mediates how pesticide exposure impacts brain gene expression in nest-founding bumble bee queens. Sci Total Environ 2022; 833:155216. [PMID: 35421476 DOI: 10.1016/j.scitotenv.2022.155216] [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: 01/19/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
A primary goal in biology is to understand the effects of multiple, interacting environmental stressors on organisms. Wild and domesticated bees are exposed to a wide variety of interacting biotic and abiotic stressors, with widespread declines in floral resources and agrochemical exposure being two of the most important. In this study, we used examinations of brain gene expression to explore the sublethal consequences of neonicotinoid pesticide exposure and pollen diet composition in nest-founding bumble bee queens. We demonstrate for the first time that pollen diet composition can influence the strength of bumble bee queen responses to pesticide exposure at the molecular level. Specifically, one pollen mixture in our study appeared to buffer bumble bee queens entirely against the effects of pesticide exposure, with respect to brain gene expression. Additionally, we detected unique effects of pollen diet and sustained (versus more temporary) pesticide exposure on queen gene expression. Our findings support the hypothesis that nutritional status can help buffer animals against the harmful effects of other stressors, including pesticides, and highlight the importance of using molecular approaches to explore sublethal consequences of stressors.
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Affiliation(s)
- Claudineia P Costa
- Department of Entomology, University of California, Riverside, Riverside, CA, USA..
| | - Mar Leza
- Department of Biology (Zoology), University of the Balearic Islands, Cra, Valldemossa, Palma, Illes Balears, Spain
| | | | - Kaleigh Fisher
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Alyssa Vollaro
- IIGB Metabolomics Core Facility, University of California, Riverside, Riverside, CA, USA
| | - Manhoi Hur
- IIGB Metabolomics Core Facility, University of California, Riverside, Riverside, CA, USA
| | - Jay S Kirkwood
- IIGB Metabolomics Core Facility, University of California, Riverside, Riverside, CA, USA
| | - S Hollis Woodard
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
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Carrillo AJ, Halilovic L, Hur M, Kirkwood JS, Borkovich KA. Targeted Metabolomics Using LC-MS in Neurospora crassa. Curr Protoc 2022; 2:e454. [PMID: 35616476 DOI: 10.1002/cpz1.454] [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: 11/07/2022]
Abstract
The filamentous fungus Neurospora crassa has historically been a model for understanding the relationship between genes and metabolism-auxotrophic mutants of N. crassa were used by Beadle and Tatum to develop the one-gene-one-enzyme hypothesis for which they earned the Nobel Prize in 1958. In the ensuing decades, several techniques have been developed for the systematic analysis of metabolites in N. crassa and other fungi. Untargeted and targeted approaches have been used, with a focus on secondary metabolites over primary metabolism. Here, we describe a pipeline for sample preparation, metabolite extraction, Liquid Chromatography-Mass Spectrometry (LC-MS), and data analysis that can be used for targeted metabolomics of primary metabolites in N. crassa. Liquid cultures are grown with shaking in a defined minimal medium and then collected using filtration. Samples are lyophilized for 2 days at -80°C, pulverized, and mixed with a solution to extract polar metabolites. The metabolites are separated and identified using LC-MS, with downstream analysis using Skyline interpretive software. Relative levels of hundreds of metabolites can be detected and compared across strains. © 2022 Wiley Periodicals LLC. Basic Protocol: Metabolite extraction and detection from Neurospora crassa cell cultures using Liquid Chromatography-Mass Spectrometry.
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Affiliation(s)
- Alexander J Carrillo
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
| | - Manhoi Hur
- Institute for Integrative Genome Biology Metabolomics Core, University of California, Riverside, California
| | - Jay S Kirkwood
- Institute for Integrative Genome Biology Metabolomics Core, University of California, Riverside, California
| | - Katherine A Borkovich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California
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Lee T, Chung H, Chung J, Hur M, Hwang S, Song Y, Lee D. M168 Automation of harboe method for the measurement of plasma free hemoglobin. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.050] [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: 11/27/2022]
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Kim H, Yoon S, Yun Y, Hur M, Moon H. M222 Evaluation of commutability of external quality assessment material for accuracy based survey of lipid tests. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.410] [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: 11/03/2022]
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Kim H, Hur M, Kim S, Moon H, Yun Y. T248 Reference intervals for 10 platelet parameters on Mindray BC-6800 plus hematology analyzer. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.736] [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: 11/24/2022]
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Yoon S, Moon H, Yi A, Kim H, Chung H, Hur M, Yun Y, Yoo G. W071 Investigation of serial tests of quantiferon-tb gold in-tube and quantiferon-tb gold-plus in contacts to patients with active tuberculosis. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.809] [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: 11/03/2022]
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Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, De Souza A, Florens L, Niles JC, Le Roch KG. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Nat Commun 2022; 13:1275. [PMID: 35277503 PMCID: PMC8917122 DOI: 10.1038/s41467-022-28981-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Anil Bhatia
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Amancio De Souza
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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14
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Kim H, Hur M. Proenkephalin predicts organ failures, renal replacement therapy, and mortality in sepsis. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.484] [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: 11/25/2022] Open
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15
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Cho H, Lee JC, Park HY, Yang W, Nam HM, Ryu J, Oh Y, Hur M. 1064P Efficacy of a novel anti-CEACAM1 monoclonal antibody and CEACAM1 up-regulation in tumour-infiltrating lymphocytes (TILs) of cancer patients. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Singh U, Hur M, Dorman K, Wurtele ES. MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. Nucleic Acids Res 2020; 48:e23. [PMID: 31956905 PMCID: PMC7039010 DOI: 10.1093/nar/gkz1209] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The diverse and growing omics data in public domains provide researchers with tremendous opportunity to extract hidden, yet undiscovered, knowledge. However, the vast majority of archived data remain unused. Here, we present MetaOmGraph (MOG), a free, open-source, standalone software for exploratory analysis of massive datasets. Researchers, without coding, can interactively visualize and evaluate data in the context of its metadata, honing-in on groups of samples or genes based on attributes such as expression values, statistical associations, metadata terms and ontology annotations. Interaction with data is easy via interactive visualizations such as line charts, box plots, scatter plots, histograms and volcano plots. Statistical analyses include co-expression analysis, differential expression analysis and differential correlation analysis, with significance tests. Researchers can send data subsets to R for additional analyses. Multithreading and indexing enable efficient big data analysis. A researcher can create new MOG projects from any numerical data; or explore an existing MOG project. MOG projects, with history of explorations, can be saved and shared. We illustrate MOG by case studies of large curated datasets from human cancer RNA-Seq, where we identify novel putative biomarker genes in different tumors, and microarray and metabolomics data from Arabidopsis thaliana. MOG executable and code: http://metnetweb.gdcb.iastate.edu/ and https://github.com/urmi-21/MetaOmGraph/.
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Affiliation(s)
- Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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17
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Lee E, Lee J, Hur M, Park HY, Yum H, Nam H, Oh MY, Choi H, Kim J, Cho B, Lim Y, Won J. MG1124, a novel CEACAM1-targeted monoclonal antibody, has therapeutic potential as a combination partner of PD-1 inhibitors in NSCLC patients. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz253.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Vliet SMF, Dasgupta S, Sparks NRL, Kirkwood JS, Vollaro A, Hur M, Zur Nieden NI, Volz DC. Maternal-to-zygotic transition as a potential target for niclosamide during early embryogenesis. Toxicol Appl Pharmacol 2019. [PMID: 31398420 DOI: 10.1016/j.taap.2019.114699,114699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Niclosamide is an antihelminthic drug used worldwide for the treatment of tapeworm infections. Recent drug repurposing screens have highlighted the broad bioactivity of niclosamide across diverse mechanisms of action. As a result, niclosamide is being evaluated for a range of alternative drug-repurposing applications, including the treatment of cancer, bacterial infections, and Zika virus. As new applications of niclosamide will require non-oral delivery routes that may lead to exposure in utero, it is important to understand the mechanism of niclosamide toxicity during early stages of embryonic development. Previously, we showed that niclosamide induces a concentration-dependent delay in epiboly progression in the absence of effects on oxidative phosphorylation - a well-established target for niclosamide. Therefore, the overall objective of this study was to further examine the mechanism of niclosamide-induced epiboly delay during zebrafish embryogenesis. Based on this study, we found that (1) niclosamide exposure during early zebrafish embryogenesis resulted in a decrease in yolk sac integrity with a concomitant decrease in the presence of yolk sac actin networks and increase in cell size; (2) within whole embryos, niclosamide exposure did not alter non-polar metabolites and lipids, but significantly altered amino acids specific to aminoacyl-tRNA biosynthesis; (3) niclosamide significantly altered transcripts related to translation, transcription, and mRNA processing pathways; and (4) niclosamide did not significantly alter levels of rRNA and tRNA. Overall, our findings suggest that niclosamide may be causing a systemic delay in embryonic development by disrupting the translation of maternally-supplied mRNAs, an effect that may be mediated through disruption of aminoacyl-tRNA biosynthesis.
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Affiliation(s)
- Sara M F Vliet
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA; Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Subham Dasgupta
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Nicole R L Sparks
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, CA, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Alyssa Vollaro
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Nicole I Zur Nieden
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, CA, USA
| | - David C Volz
- Department of Environmental Sciences, University of California, Riverside, CA, USA.
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19
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Dasgupta S, Vliet SMF, Cheng V, Mitchell CA, Kirkwood J, Vollaro A, Hur M, Mehdizadeh C, Volz DC. Complex Interplay Among Nuclear Receptor Ligands, Cytosine Methylation, and the Metabolome in Driving Tris(1,3-dichloro-2-propyl)phosphate-Induced Epiboly Defects in Zebrafish. Environ Sci Technol 2019; 53:10497-10505. [PMID: 31385694 PMCID: PMC6721996 DOI: 10.1021/acs.est.9b04127] [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] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) is a high-production-volume organophosphate flame retardant (OPFR) that induces epiboly defects during zebrafish embryogenesis, leading to the disruption of dorsoventral patterning. Therefore, the objectives of this study were to (1) identify the potential mechanisms involved in TDCIPP-induced epiboly defects and (2) determine whether coexposure to triphenyl phosphate (TPHP)-an OPFR commonly detected with TDCIPP-enhances or mitigates epiboly defects. Although TDCIPP-induced epiboly defects were not associated with adverse impacts on cytoskeletal protein abundance in situ, the coexposure of embryos to TPHP partially blocked TDCIPP-induced epiboly defects. As nuclear receptors are targets for both TPHP and TDCIPP, we exposed the embryos to TDCIPP in the presence or absence of 69 nuclear receptor ligands and, similar to TPHP, found that ciglitazone (a peroxisome proliferator-activated receptor γ agonist) and 17β-estradiol (E2; an estrogen receptor α agonist) nearly abolished TDCIPP-induced epiboly defects. Moreover, E2 and ciglitazone mitigated TDCIPP-induced effects on CpG hypomethylation within the target loci prior to epiboly, and ciglitazone altered TDCIPP-induced effects on the abundance of two polar metabolites (acetylcarnitine and cytidine-5-diphosphocholine) during epiboly. Overall, our results point to a complex interplay among nuclear receptor ligands, cytosine methylation, and the metabolome in both the induction and mitigation of epiboly defects induced by TDCIPP.
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Affiliation(s)
- Subham Dasgupta
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
| | - Sara M. F. Vliet
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
| | - Vanessa Cheng
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
| | - Constance A. Mitchell
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
| | - Jay Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Alyssa Vollaro
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Chris Mehdizadeh
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
| | - David C. Volz
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
- Phone: (951) 827-4450; Fax: (951) 827-4652;
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20
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Vliet SMF, Dasgupta S, Sparks NRL, Kirkwood JS, Vollaro A, Hur M, Zur Nieden NI, Volz DC. Maternal-to-zygotic transition as a potential target for niclosamide during early embryogenesis. Toxicol Appl Pharmacol 2019; 380:114699. [PMID: 31398420 DOI: 10.1016/j.taap.2019.114699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/25/2019] [Revised: 07/16/2019] [Accepted: 08/04/2019] [Indexed: 12/31/2022]
Abstract
Niclosamide is an antihelminthic drug used worldwide for the treatment of tapeworm infections. Recent drug repurposing screens have highlighted the broad bioactivity of niclosamide across diverse mechanisms of action. As a result, niclosamide is being evaluated for a range of alternative drug-repurposing applications, including the treatment of cancer, bacterial infections, and Zika virus. As new applications of niclosamide will require non-oral delivery routes that may lead to exposure in utero, it is important to understand the mechanism of niclosamide toxicity during early stages of embryonic development. Previously, we showed that niclosamide induces a concentration-dependent delay in epiboly progression in the absence of effects on oxidative phosphorylation - a well-established target for niclosamide. Therefore, the overall objective of this study was to further examine the mechanism of niclosamide-induced epiboly delay during zebrafish embryogenesis. Based on this study, we found that (1) niclosamide exposure during early zebrafish embryogenesis resulted in a decrease in yolk sac integrity with a concomitant decrease in the presence of yolk sac actin networks and increase in cell size; (2) within whole embryos, niclosamide exposure did not alter non-polar metabolites and lipids, but significantly altered amino acids specific to aminoacyl-tRNA biosynthesis; (3) niclosamide significantly altered transcripts related to translation, transcription, and mRNA processing pathways; and (4) niclosamide did not significantly alter levels of rRNA and tRNA. Overall, our findings suggest that niclosamide may be causing a systemic delay in embryonic development by disrupting the translation of maternally-supplied mRNAs, an effect that may be mediated through disruption of aminoacyl-tRNA biosynthesis.
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Affiliation(s)
- Sara M F Vliet
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA; Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Subham Dasgupta
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Nicole R L Sparks
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, CA, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Alyssa Vollaro
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Nicole I Zur Nieden
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, CA, USA
| | - David C Volz
- Department of Environmental Sciences, University of California, Riverside, CA, USA.
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21
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Reddam A, Mitchell CA, Dasgupta S, Kirkwood JS, Vollaro A, Hur M, Volz DC. mRNA-Sequencing Identifies Liver as a Potential Target Organ for Triphenyl Phosphate in Embryonic Zebrafish. Toxicol Sci 2019; 172:51-62. [PMID: 31368501 PMCID: PMC6813745 DOI: 10.1093/toxsci/kfz169] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/03/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 01/01/2023] Open
Abstract
Triphenyl phosphate (TPHP) is a commonly used organophosphate flame retardant and plasticizer in the United States. Using zebrafish as a model, the overall objective of this study was to identify potential organs that might be targeted by TPHP during embryonic development. Based on mRNA-sequencing, TPHP exposure from 24 to 30 h post fertilization (hpf) and 24 to 48 hpf significantly affected the abundance of 305 and 274 transcripts, respectively, relative to vehicle (0.1% DMSO) controls. In addition to minor effects on cardiotoxicity- and nephrotoxicity-related pathways, Ingenuity Pathway Analysis (IPA) of significantly affected transcripts within 30- and 48-hpf embryos revealed that hepatotoxicity-related pathways were strongly affected following exposure to TPHP alone. Moreover, while pre-treatment with fenretinide (a retinoic acid receptor agonist) mitigated TPHP-induced pericardial edema and liver enlargement at 72 hpf and 128 hpf, respectively, IPA revealed that fenretinide was unable to block TPHP-induced effects on cardiotoxicity-, nephrotoxicity-, and hepatotoxicity-related pathways at 48 hpf, suggesting that TPHP-induced effects on the transcriptome were not associated with toxicity later in development. In addition, based on Oil Red O staining, we found that exposure to TPHP nearly abolished neutral lipids from the embryonic head and trunk and, based on metabolomics, significantly decreased the total abundance of metabolites - including betaine, a known osmoprotectant - at 48 and 72 hpf. Overall, our data suggest that, in addition to the heart, TPHP exposure during early development results in adverse effects on the liver, lipid utilization, and osmoregulation within embryonic zebrafish.
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Affiliation(s)
- Aalekhya Reddam
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.,Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Constance A Mitchell
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.,Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Subham Dasgupta
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Alyssa Vollaro
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - David C Volz
- Department of Environmental Sciences, University of California, Riverside, CA, USA
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22
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Cho E, Park M, Hur M, Kang G, Kim YH, Kim S. Molecular-level investigation of soils contaminated by oil spilled during the Gulf War. J Hazard Mater 2019; 373:271-277. [PMID: 30925386 DOI: 10.1016/j.jhazmat.2019.03.084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
In this study, molecular-level chemical compositions of soils contaminated by oil spilled during the Gulf War were studied. Two soil samples, respectively collected at 0.1 m and between 0.5 and 1 m below the surface from an oil spill site, were extracted with organic solvents and water. The extracts were analyzed via ultrahigh resolution FT-ICR and two-dimensional gas chromatography/high resolution mass spectrometry. The data showed that the spilled oil was significantly affected by vaporization due to high surface temperatures in the desert. The data obtained with (+) atmospheric pressure photo ionization (APPI) and (-) electrospray ionization (ESI) coupled with ultrahigh resolution-mass spectrometry (UHR-MS) indicated that the degradation of aromatic compounds and increase in oxygen-containing classes occurred in the following order: surface soil > below surface soil > crude oil. The oxygenated compounds were confirmed by principal component analysis. The score and loading plots of Ox and SOx showed that they were the major contributors to differentiate the samples. However, a comparison with previously reported oceanic oil spills showed that less significant degradation occurred even after almost 30 years. Our data can provide an information basis for designing a strategy for clean-up and restoration efforts of Gulf War oil spills.
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Affiliation(s)
- Eunji Cho
- Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Moonhee Park
- Biomedical Omics Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Cheongju, Chungcheongbuk-do 28119, Republic of Korea
| | - Manhoi Hur
- Department of Botany and Plant Sciences, and Institute of Integrative Genome Biology, University of California, Riverside, CA 92506, United States
| | - Guyoung Kang
- Department of Environmental Sciences, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeon-eup, Cheoin-gu 17035, Republic of Korea.
| | - Young Hwan Kim
- Biomedical Omics Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Cheongju, Chungcheongbuk-do 28119, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; Green-Nano Materials Research Center, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.
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23
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Jun Young Y, Vyas C, Hur M, Yang S, Kong Y, Lee E, Song H, Park J. Overcoming immune-barrier: cell membrane cloaked zirconium-89 hollow mesoporous silica nanospheres. Nucl Med Biol 2019. [DOI: 10.1016/s0969-8051(19)30307-5] [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: 10/26/2022]
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24
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Choi P, Lee J, Vyas C, Gong Y, Lee E, Song H, Yang S, Hur M, Kim S, Park J. 89Zr-incorporated iron oxide nanocluster by chelator-free simple direct-labelling method for PET diagnosis. Nucl Med Biol 2019. [DOI: 10.1016/s0969-8051(19)30361-0] [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: 11/30/2022]
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25
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Kim W, Hur M, Park SK, Yoo S, Lim T, Yoon H, Kim JT, Bahk JH. Comparison between general, spinal, epidural, and combined spinal-epidural anesthesia for cesarean delivery: a network meta-analysis. Int J Obstet Anesth 2019; 37:5-15. [DOI: 10.1016/j.ijoa.2018.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/12/2018] [Accepted: 09/21/2018] [Indexed: 12/18/2022]
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26
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Kim WH, Hur M, Park SK, Jung DE, Kang P, Yoo S, Bahk JH. Pharmacological interventions for protecting renal function after cardiac surgery: a Bayesian network meta-analysis of comparative effectiveness. Anaesthesia 2018; 73:1019-1031. [DOI: 10.1111/anae.14227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2018] [Indexed: 12/25/2022]
Affiliation(s)
- W. H. Kim
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
| | - M. Hur
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
| | - S.-K. Park
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
| | - D. E. Jung
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
| | - P. Kang
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
| | - S. Yoo
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
| | - J.-H. Bahk
- Department of Anesthesiology and Pain Medicine; Seoul National University Hospital; Seoul Korea
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27
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Reem NT, Chen HY, Hur M, Zhao X, Wurtele ES, Li X, Li L, Zabotina O. Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations. Plant Mol Biol 2018; 96:509-529. [PMID: 29502299 DOI: 10.1007/s11103-018-0714-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 10/12/2017] [Accepted: 02/25/2018] [Indexed: 06/08/2023]
Abstract
This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.
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Affiliation(s)
- Nathan T Reem
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, USA
| | - Han-Yi Chen
- Plants for Human Health Institute, North Carolina State University, Kannapolis, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Manhoi Hur
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, USA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, USA
- Information Technology, College of Liberal Arts and Sciences, Iowa State University, Ames, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, USA
| | - Xu Li
- Plants for Human Health Institute, North Carolina State University, Kannapolis, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Ling Li
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, USA
- Department of Biological Sciences, Mississippi State University, Starkville, USA
| | - Olga Zabotina
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, USA.
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Bhandary P, Seetharam AS, Arendsee ZW, Hur M, Wurtele ES. Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data. Plant Sci 2018; 267:32-47. [PMID: 29362097 DOI: 10.1016/j.plantsci.2017.10.014] [Citation(s) in RCA: 9] [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: 07/17/2017] [Revised: 10/07/2017] [Accepted: 10/15/2017] [Indexed: 05/19/2023]
Abstract
More than 15 petabases of raw RNAseq data is now accessible through public repositories. Acquisition of other 'omics data types is expanding, though most lack a centralized archival repository. Data-reuse provides tremendous opportunity to extract new knowledge from existing experiments, and offers a unique opportunity for robust, multi-'omics analyses by merging metadata (information about experimental design, biological samples, protocols) and data from multiple experiments. We illustrate how predictive research can be accelerated by meta-analysis with a study of orphan (species-specific) genes. Computational predictions are critical to infer orphan function because their coding sequences provide very few clues. The metadata in public databases is often confusing; a test case with Zea mays mRNA seq data reveals a high proportion of missing, misleading or incomplete metadata. This metadata morass significantly diminishes the insight that can be extracted from these data. We provide tips for data submitters and users, including specific recommendations to improve metadata quality by more use of controlled vocabulary and by metadata reviews. Finally, we advocate for a unified, straightforward metadata submission and retrieval system.
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Affiliation(s)
- Priyanka Bhandary
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Zebulun W Arendsee
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA.
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Park SK, Hur M, Yoo S, Choi JY, Kim WH, Kim JT, Bahk JH. Effect of remote ischaemic preconditioning in patients with ischaemic heart disease undergoing orthopaedic surgery: a randomized controlled trial. Br J Anaesth 2017; 120:198-200. [PMID: 29397131 DOI: 10.1016/j.bja.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 08/22/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022] Open
Affiliation(s)
- S-K Park
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - M Hur
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - S Yoo
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - J-Y Choi
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - W H Kim
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - J-T Kim
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - J-H Bahk
- Department of Anesthesiology and Pain Medicine, Seoul National University Hospital, Seoul, Republic of Korea
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Affiliation(s)
- Eunji Cho
- Department
of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Matthias Witt
- Bruker Daltonik
GmbH, Fahrenheitrasse 4, 28359 Bremen, Germany
| | - Manhoi Hur
- Department
of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, United States
- Center
for Metabolic Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Maeng-Joon Jung
- Department
of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Sunghwan Kim
- Department
of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Green-Nano Materials
Research Center, Daegu 41566, Republic of Korea
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Hur M, Lee HC, Lee KH, Kim JT, Jung CW, Park HP. The incidence and characteristics of 3-month mortality after intraoperative cardiac arrest in adults. Acta Anaesthesiol Scand 2017; 61:1095-1104. [PMID: 28799206 DOI: 10.1111/aas.12955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 03/09/2017] [Revised: 07/20/2017] [Accepted: 07/22/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND There is little information about clinical outcomes after intraoperative cardiac arrest (IOCA). We determined the incidence and characteristics of 3-month mortality after IOCA. METHODS The electronic medical records of 238,648 adult surgical patients from January 2005 to December 2014 were reviewed retrospectively. Characteristics of IOCA were documented using the Utstein reporting template. RESULTS IOCA occurred in 50 patients (21/100,000 surgeries). Nineteen patients died in the operating room, and further 12 patients died within 3 months post-arrest (total mortality: 62%). Three survivors at 3 months post-arrest had unfavourable neurological outcome. Finally, 34 patients showed unfavourable clinical outcomes at 3 months post-arrest. The incidences of non-cardiac surgery, emergency, pre-operative intubation state, non-shockable initial cardiac rhythm, hypovolaemic shock, pre-operative complications-induced cardiac arrest, non-anaesthetic cause of cardiac arrest, intra- and post-arrest transfusion, and continuous infusion of inotrope or vasopressor in intensive care unit (ICU) were significantly higher in non-survivors at 3 months post-arrest. Total epinephrine dose administrated during arrest was higher, and the duration of cardiac compressions was longer in non-survivors at 3 months post-arrest. CONCLUSIONS In this study, the incidence of IOCA was 21/100,000 surgeries and the 3-month mortality rate after IOCA was 62%. Several factors including surgical emergency, non-shockable initial cardiac rhythm, pre-operative complications, surgical complications, long duration of cardiac compressions, high total epinephrine dose, transfusion, and continuous infusion of inotropes or vasopressors in ICU seemed to be risk factors for 3-month mortality after IOCA. These risk factors should be considered in the light of relatively small sample size of this study.
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Affiliation(s)
- M. Hur
- Department of Anaesthesiology and Pain Medicine; Seoul National University Hospital; Seoul National University College of Medicine; Seoul Korea
| | - H.-C. Lee
- Department of Anaesthesiology and Pain Medicine; Seoul National University Hospital; Seoul National University College of Medicine; Seoul Korea
| | - K. H. Lee
- Department of Anaesthesiology and Pain Medicine; Seoul National University Hospital; Seoul National University College of Medicine; Seoul Korea
| | - J.-T. Kim
- Department of Anaesthesiology and Pain Medicine; Seoul National University Hospital; Seoul National University College of Medicine; Seoul Korea
| | - C.-W. Jung
- Department of Anaesthesiology and Pain Medicine; Seoul National University Hospital; Seoul National University College of Medicine; Seoul Korea
| | - H.-P. Park
- Department of Anaesthesiology and Pain Medicine; Seoul National University Hospital; Seoul National University College of Medicine; Seoul Korea
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32
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Islam A, Ahmed A, Hur M, Thorn K, Kim S. Molecular-level evidence provided by ultrahigh resolution mass spectrometry for oil-derived doc in groundwater at Bemidji, Minnesota. J Hazard Mater 2016; 320:123-132. [PMID: 27526278 DOI: 10.1016/j.jhazmat.2016.08.018] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 06/06/2023]
Abstract
Dissolved organic matter samples extracted from ground water at the USGS Bemidji oil spill site in Minnesota were investigated by ultrahigh resolution mass spectrometry. Principle component analysis (PCA) of the elemental composition assignments of the samples showed that the score plots for the contaminated sites were well separated from those for the uncontaminated sites. Additionally, spectra obtained from the same sampling site 7 and 19 years after the spill were grouped together in the score plot, strongly suggesting a steady state of contamination within the 12year interval. The double bond equivalence (DBE) of Ox class compounds was broader for the samples from the contaminated sites, because of the complex nature of oil and the consequent formation of compounds with saturated and/or aromatic structures from the oxygenated products of oil. In addition, Ox class compounds with a relatively smaller number of x (x<8; x=number of oxygen) and OxS1 class compounds were more abundant in the samples from the contaminated sites, because of the lower oxygen and higher sulfur contents of the oil compared to humic substances. The molecular-level signatures presented here can be a fundamental basis for in-depth analysis of oil contamination.
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Affiliation(s)
- Ananna Islam
- Kyungpook National University, Department of Chemistry, Daegu 702-701, Republic of Korea
| | - Arif Ahmed
- Kyungpook National University, Department of Chemistry, Daegu 702-701, Republic of Korea
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Kevin Thorn
- Water Mission Area, U.S. Geological Survey, Denver, CO 80225, USA
| | - Sunghwan Kim
- Kyungpook National University, Department of Chemistry, Daegu 702-701, Republic of Korea; Green Nano Center, Department of Chemistry, Daegu 702-701, Republic of Korea.
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Rizhsky L, Jin H, Shepard MR, Scott HW, Teitgen AM, Perera MA, Mhaske V, Jose A, Zheng X, Crispin M, Wurtele ES, Jones D, Hur M, Góngora-Castillo E, Buell CR, Minto RE, Nikolau BJ. Integrating metabolomics and transcriptomics data to discover a biocatalyst that can generate the amine precursors for alkamide biosynthesis. Plant J 2016; 88:775-793. [PMID: 27497272 PMCID: PMC5195896 DOI: 10.1111/tpj.13295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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] [Received: 03/30/2016] [Revised: 06/30/2016] [Accepted: 08/02/2016] [Indexed: 05/03/2023]
Abstract
The Echinacea genus is exemplary of over 30 plant families that produce a set of bioactive amides, called alkamides. The Echinacea alkamides may be assembled from two distinct moieties, a branched-chain amine that is acylated with a novel polyunsaturated fatty acid. In this study we identified the potential enzymological source of the amine moiety as a pyridoxal phosphate-dependent decarboxylating enzyme that uses branched-chain amino acids as substrate. This identification was based on a correlative analysis of the transcriptomes and metabolomes of 36 different E. purpurea tissues and organs, which expressed distinct alkamide profiles. Although no correlation was found between the accumulation patterns of the alkamides and their putative metabolic precursors (i.e., fatty acids and branched-chain amino acids), isotope labeling analyses supported the transformation of valine and isoleucine to isobutylamine and 2-methylbutylamine as reactions of alkamide biosynthesis. Sequence homology identified the pyridoxal phosphate-dependent decarboxylase-like proteins in the translated proteome of E. purpurea. These sequences were prioritized for direct characterization by correlating their transcript levels with alkamide accumulation patterns in different organs and tissues, and this multi-pronged approach led to the identification and characterization of a branched-chain amino acid decarboxylase, which would appear to be responsible for generating the amine moieties of naturally occurring alkamides.
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Affiliation(s)
- Ludmila Rizhsky
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa, USA
| | - Huanan Jin
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa, USA
| | - Michael R. Shepard
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| | - Harry W. Scott
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| | - Alicen M. Teitgen
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| | - M. Ann Perera
- W.M. Keck Metabolomics Research Laboratory, Iowa State University, Ames, Iowa, USA
| | - Vandana Mhaske
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Adarsh Jose
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa, USA
| | - Xiaobin Zheng
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Matt Crispin
- Department of Genetics, Development & Cell Biology-LAS, Iowa State University, Ames, Iowa, USA
| | - Eve S. Wurtele
- Department of Genetics, Development & Cell Biology-LAS, Iowa State University, Ames, Iowa, USA
| | - Dallas Jones
- Department of Genetics, Development & Cell Biology-LAS, Iowa State University, Ames, Iowa, USA
| | - Manhoi Hur
- Department of Genetics, Development & Cell Biology-LAS, Iowa State University, Ames, Iowa, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa, USA
| | | | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing MI 48824 USA
| | - Robert E. Minto
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| | - Basil J. Nikolau
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa, USA
- Corresponding Author: Basil J. Nikolau;
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34
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Trabue SL, Kerr BJ, Bearson BL, Hur M, Parkin T, Wurtele ES, Ziemer CJ. Microbial Community and Chemical Characteristics of Swine Manure during Maturation. J Environ Qual 2016; 45:1144-1152. [PMID: 27380061 DOI: 10.2134/jeq2015.09.0446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Swine diet formulations have the potential to lower animal emissions, including odor and ammonia (NH). The purpose of this study was to determine the impact of manure storage duration on manure chemical and microbial properties in swine feeding trials. Three groups of 12 pigs were fed a standard corn-soybean meal diet over a 13-wk period. Urine and feces were collected at each feeding and transferred to 12 manure storage tanks. Manure chemical characteristics and headspace gas concentrations were monitored for NH, hydrogen sulfide (HS), volatile fatty acids, phenols, and indoles. Microbial analysis of the stored manure included plate counts, community structure (denaturing gradient gel electrophoresis), and metabolic function (Biolog). All odorants in manure and headspace gas concentrations were significantly ( < 0.01) correlated for length of storage using quadratic equations, peaking after Week 5 for all headspace gases and most manure chemical characteristics. Microbial community structure and metabolic utilization patterns showed continued change throughout the 13-wk trial. Denaturing gradient gel electrophoresis species diversity patterns declined significantly ( < 0.01) with time as substrate utilization declined for sugars and certain amino acids, but functionality increased in the utilization of short chain fatty acids as levels of these compounds increased in manure. Studies to assess the effect of swine diet formulations on manure emissions for odor need to be conducted for a minimum of 5 wk. Efforts to determine the impact of diets on greenhouse gas emissions will require longer periods of study (>13 wk).
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Kim H, Hur M, Choi SG, Oh KM, Moon HW, Yun YM. Comparison of white blood cell counts by WNR, WDF, and WPC channels in Sysmex XN hematology analyzer. Int J Lab Hematol 2015; 37:869-75. [DOI: 10.1111/ijlh.12421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/31/2015] [Indexed: 11/28/2022]
Affiliation(s)
- H. Kim
- Department of Laboratory Medicine; Konkuk University School of Medicine; Seoul Korea
| | - M. Hur
- Department of Laboratory Medicine; Konkuk University School of Medicine; Seoul Korea
| | - S.-G. Choi
- Department of Laboratory Medicine; Konkuk University School of Medicine; Seoul Korea
| | - K.-M. Oh
- Department of Nursing; Konkuk University Medical Center; Seoul Korea
| | - H.-W. Moon
- Department of Laboratory Medicine; Konkuk University School of Medicine; Seoul Korea
| | - Y.-M. Yun
- Department of Laboratory Medicine; Konkuk University School of Medicine; Seoul Korea
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36
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Ji M, Hur M, Kim HN, Moon HW, Yun YM, Kim SY. Abrupt thrombocytopenia with sustained trilineage engraftment in a stem cell transplant recipient. Int J Lab Hematol 2015; 37:e106-8. [PMID: 25754932 DOI: 10.1111/ijlh.12338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Ji
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - M Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea.
| | - H N Kim
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - H-W Moon
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Y-M Yun
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - S-Y Kim
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
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Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. BMC Genomics 2015; 16 Suppl 3:S9. [PMID: 25708381 PMCID: PMC4331812 DOI: 10.1186/1471-2164-16-s3-s9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. RESULTS With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. CONCLUSIONS This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Affiliation(s)
- Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Joon-Yong Lee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Wenxu Zhou
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Zhihong Song
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Nick Ransom
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark Westgate
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Vidya Iyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jackie Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Basil Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
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Vu HS, Roston R, Shiva S, Hur M, Wurtele ES, Wang X, Shah J, Welti R. Modifications of membrane lipids in response to wounding of Arabidopsis thaliana leaves. Plant Signal Behav 2015; 10:e1056422. [PMID: 26252884 PMCID: PMC4883853 DOI: 10.1080/15592324.2015.1056422] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 05/05/2023]
Abstract
Mechanical wounding of Arabidopsis thaliana leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
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Affiliation(s)
- Hieu Sy Vu
- Kansas Lipidomics Research Center; Division of Biology; Kansas State University; Manhattan, KS USA
- Department of Biochemistry and Center for Plant Science Innovation; University of Nebraska-Lincoln; Lincoln, NE USA
| | - Rebecca Roston
- Department of Biochemistry and Center for Plant Science Innovation; University of Nebraska-Lincoln; Lincoln, NE USA
| | - Sunitha Shiva
- Kansas Lipidomics Research Center; Division of Biology; Kansas State University; Manhattan, KS USA
| | - Manhoi Hur
- Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, IA USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, IA USA
| | - Xuemin Wang
- Department of Biology; University of Missouri; Donald Danforth Plant Science Center; St. Louis, MO USA
| | - Jyoti Shah
- Department of Biological Sciences; University of North Texas; Denton, TX USA
| | - Ruth Welti
- Kansas Lipidomics Research Center; Division of Biology; Kansas State University; Manhattan, KS USA
- Correspondence to: Ruth Welti;
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Fukushima A, Kusano M, Mejia RF, Iwasa M, Kobayashi M, Hayashi N, Watanabe-Takahashi A, Narisawa T, Tohge T, Hur M, Wurtele ES, Nikolau BJ, Saito K. Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis. Plant Physiol 2014; 165:948-961. [PMID: 24828308 PMCID: PMC4081348 DOI: 10.1104/pp.114.240986] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/05/2014] [Indexed: 05/19/2023]
Abstract
Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally, and improving gene annotation remains a major challenge in plant science. As metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation in the plant metabolism, it provides clues to the function(s) of genes of interest. We chose 50 Arabidopsis mutants, including a set of characterized and uncharacterized mutants, that resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry. To make the data set available as an efficient public functional genomics tool for hypothesis generation, we developed the Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). It allows the evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools. Nonprocessed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by the Metabolomics Standards Initiative and are freely downloadable. Proof-of-concept analysis suggests that MeKO is highly useful for the generation of hypotheses for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.riken.jp/meko/.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Ramon Francisco Mejia
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Mami Iwasa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Naomi Hayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Akiko Watanabe-Takahashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Tomoko Narisawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Takayuki Tohge
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Manhoi Hur
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Eve Syrkin Wurtele
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Basil J Nikolau
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
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Crispin MC, Hur M, Park T, Kim YH, Wurtele ES. Identification and biosynthesis of acylphloroglucinols in Hypericum gentianoides. Physiol Plant 2013; 148:354-70. [PMID: 23600727 PMCID: PMC3687794 DOI: 10.1111/ppl.12063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/05/2013] [Accepted: 04/10/2013] [Indexed: 05/18/2023]
Abstract
Species of the genus Hypericum contain a rich array of unusual polyketides, however, only a small proportion of the over 450 Hypericum species, other than the popular medicinal supplement St. John's Wort (Hypericum perforatum), have even been chemically characterized. Hypericum gentianoides, a small annual used medicinally by Cherokee Americans, contains bioactive acylphloroglucinols. Here, we identify acylphloroglucinol constituents of H. gentianoides and determine a potential pathway to their synthesis. Liquid chromatography/electrospray ionization-mass spectrometry (LC/ESI-MS) and HPLC-UV indicate that the level of accumulation and profile of acylphloroglucinols in H. gentianoides vary little seasonally when grown in a greenhouse, but do vary with development and are highly dependent on the accession, highlighting the importance of the selection of plant material for study. We identify the chemical structures of the nine prevalent polyketides, based on LC/ESI-MS and hybrid quadrupole orthogonal time-of-flight (Q-TOF) mass spectrometry; these metabolites include one monomeric phlorisobutyrophenone (PIB) derivative and eight dimeric acylphloroglucinols. Q-TOF spectrometry was used to identify eight additional PIB derivatives that were not detected by LC/ESI-MS. These data lead us to propose that diacylphloroglucinols are synthesized via modification of PIB to yield diverse phloroglucinol and filicinic acids moieties, followed by dimerization of a phloroglucinol and a filicinic acid monomer to yield the observed complement of diacylphloroglucinols. The metabolomics data from H. gentianoides are accessible in plant metabolomics resource (PMR) (http://www.metnetdb.org/pmr), a public metabolomics database with analysis software for plants and microbial organisms.
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Affiliation(s)
- Matthew C. Crispin
- Department of Genetics, Developmental, and Cell Biology, Iowa State University USA
| | - Manhoi Hur
- Department of Genetics, Developmental, and Cell Biology, Iowa State University USA
| | - Taeseong Park
- Division of Mass Spectrometry Research, Korea Basic Science Institute, Ochang 863-883, Korea
| | - Young Hwan Kim
- Division of Mass Spectrometry Research, Korea Basic Science Institute, Ochang 863-883, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Eve Syrkin Wurtele
- Department of Genetics, Developmental, and Cell Biology, Iowa State University USA
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Kim H, Hur M, Choi SG, Kim BH, Moon HW, Yun YM, Hwang HS, Kwon HS, Sohn IS. Evaluation of ABX Pentra DX 120 and Sysmex XE-2100 in umbilical cord blood. Int J Lab Hematol 2013; 35:658-65. [PMID: 23738834 DOI: 10.1111/ijlh.12110] [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] [Received: 02/25/2013] [Accepted: 04/15/2013] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Cord blood (CB) is an important source of hematopoietic stem cells and reflects the hematologic status of neonates. ABX Pentra DX 120 (Horiba Medical, Montpellier, France) and Sysmex XE-2100 (Sysmex, Kobe, Japan) were compared in 200 CB specimens. METHODS Complete blood count parameters including white blood cell (WBC) differential counts were compared between the two analyzers. Double differential matrix (DDX) by ABX Pentra DX 120 and hematopoietic progenitor cell (HPC) by Sysmex XE-2100 were compared with CD34(+) cells by flow cytometry. RESULTS Most of the parameters showed acceptable correlation between the two analyzers. Although WBC differential of both analyzers showed acceptable correlation with manual counts, mononuclear cells (MNC) by ABX Pentra DX 120 better correlated with manual count than MNC by Sysmex XE-2100. NRBC by Sysmex XE-2100 better correlated with manual count than NRBC by ABX Pentra DX 120. ABX Pentra DX 120 showed better flagging performances. DDX better correlated with CD34(+) cells than HPC. CONCLUSION Although the results from both analyzers are mostly interchangeable and reliable in CB specimens, flagging performance of ABX Pentra DX 120 seems to be superior to that of Sysmex XE-2100. DDX by ABX Pentra DX 120 would be valuable to evaluate the quality of CB for further therapeutic utilization.
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Affiliation(s)
- H Kim
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
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Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES. A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat Prod Rep 2013; 30:565-83. [PMID: 23447050 PMCID: PMC3629923 DOI: 10.1039/c3np20111b] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Discovering molecular components and their functionality is key to the development of hypotheses concerning the organization and regulation of metabolic networks. The iterative experimental testing of such hypotheses is the trajectory that can ultimately enable accurate computational modelling and prediction of metabolic outcomes. This information can be particularly important for understanding the biology of natural products, whose metabolism itself is often only poorly defined. Here, we describe factors that must be in place to optimize the use of metabolomics in predictive biology. A key to achieving this vision is a collection of accurate time-resolved and spatially defined metabolite abundance data and associated metadata. One formidable challenge associated with metabolite profiling is the complexity and analytical limits associated with comprehensively determining the metabolome of an organism. Further, for metabolomics data to be efficiently used by the research community, it must be curated in publicly available metabolomics databases. Such databases require clear, consistent formats, easy access to data and metadata, data download, and accessible computational tools to integrate genome system-scale datasets. Although transcriptomics and proteomics integrate the linear predictive power of the genome, the metabolome represents the nonlinear, final biochemical products of the genome, which results from the intricate system(s) that regulate genome expression. For example, the relationship of metabolomics data to the metabolic network is confounded by redundant connections between metabolites and gene-products. However, connections among metabolites are predictable through the rules of chemistry. Therefore, enhancing the ability to integrate the metabolome with anchor-points in the transcriptome and proteome will enhance the predictive power of genomics data. We detail a public database repository for metabolomics, tools and approaches for statistical analysis of metabolomics data, and methods for integrating these datasets with transcriptomic data to create hypotheses concerning specialized metabolisms that generate the diversity in natural product chemistry. We discuss the importance of close collaborations among biologists, chemists, computer scientists and statisticians throughout the development of such integrated metabolism-centric databases and software.
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Affiliation(s)
- Manhoi Hur
- Human Computer Interactions and Department of Genetics Development and Cell Biology, 2624 Howe Hall, Iowa State University, Ames, IA 50011, USA. Fax: +1 515 294 0803; Tel: +1 515 708 3232;
| | - Alexis Ann Campbell
- Biochemistry, Biophysics and Molecular Biology and Center for Biorenewable Chemicals and Center for Metabolic Biology, 3254 Molecular Biology Building, Iowa State University, Ames, IA 50010, USA. Fax: +1 515 294 9423; Tel: +1 515 294 0453;
| | - Marcia Almeida-de-Macedo
- Department of Genetics Development and Cell Biology, 2624 Howe Hall, Iowa State University, Ames, IA 50011, USA. Fax: +1 515 294 5530; Tel: +1 515 294 3738;
| | - Ling Li
- Department of Genetics Development and Cell Biology, 443 Bessey Hall Iowa State University, Ames, IA 50011, USA. Fax: +1 515 294 1337; Tel: +1 515 294 6236;
| | - Nick Ransom
- Department of Genetics Development and Cell Biology, 2624 Howe Hall, Iowa State University, Ames, IA 50011, USA. Fax: +1 515 294 0803; Tel: +1 515 708 3232;
| | - Adarsh Jose
- Bioinformatics and Computational Biology, Center for Biorenewable Chemicals, Iowa State University, Ames, IA 50010, USA. Fax: +1 515 294 1269; Tel: +1 515 230 3429;
| | - Matt Crispin
- Department of Genetics Development and Cell Biology, 443 Bessey Hall Iowa State University, Ames, IA 50011, USA. Fax: +1 515 294 1337; Tel: +1 515 294 6236;
| | - Basil J. Nikolau
- Biochemistry, Biophysics and Molecular Biology and Center for Biorenewable Chemicals and Center for Metabolic Biology, 3254 Molecular Biology Building, Iowa State University, Ames, IA 50010, USA. Fax: +1 515 294 9423; Tel: +1 515 294 0453;
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Center for Metabolic Biology, and Center for Biorenewable Chemicals, 2624D Howe Hall, Iowa State University, Ames, IA 50011, USA. Fax: +1 515 294 0803; Tel: +1 515 708 3232;
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Ko YJ, Kim H, Hur M, Choi SG, Moon HW, Yun YM, Hong SN. Establishment of reference interval for immature platelet fraction. Int J Lab Hematol 2013; 35:528-33. [PMID: 23286350 DOI: 10.1111/ijlh.12049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 10/04/2012] [Accepted: 11/28/2012] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Immature platelet fraction (IPF) is a parameter for reticulated platelets. A high percentage IPF (%-IPF) is indicative of consumptive or recovering thrombocytopenic disorders in contrast to a low %-IPF seen in aplastic states. Absolute IPF (A-IPF) specifically reflects the number of immature platelets in circulation. This study aimed to establish reliable reference intervals for %-IPF and A-IPF. METHODS Except outliers, platelet counts and IPF were determined in 2152 healthy individuals (1252 men and 900 women) and 133 umbilical cord blood from healthy full-term neonates using XE-2100 hematology analyzer (Sysmex, Kobe, Japan). The reference intervals for %-IPF and A-IPF were defined using nonparametrical percentile methods according to the Clinical and Laboratory Standard Institute (CLSI) guideline. RESULTS Platelets,%-IPF, and A-IPF all showed nonparametrical distributions. In total individuals, the reference intervals for %-IPF and A-IPF were 0.5-3.3% (0.5-3.1% in men; 0.5-3.4% in women) and 1.25-7.02 × 10(9) /L (1.30-6.80 × 10(9) /L in men; 1.21-7.15 × 10(9) /L in women), respectively. The reference intervals for %-IPF and A-IPF in umbilical cord blood were 0.7-3.8% and 1.93-9.7 × 10(9) /L, respectively. CONCLUSIONS This study provides the reference interval for IPF, including %-IPF and A-IPF, according to the CLSI guideline. These results could be used as fundamental data for clinical use as well as future researches.
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Affiliation(s)
- Y J Ko
- Departments of Laboratory Medicine and Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
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Wurtele ES, Chappell J, Jones AD, Celiz MD, Ransom N, Hur M, Rizshsky L, Crispin M, Dixon P, Liu J, P Widrlechner M, Nikolau BJ. Medicinal plants: a public resource for metabolomics and hypothesis development. Metabolites 2012; 2:1031-59. [PMID: 24957774 PMCID: PMC3901233 DOI: 10.3390/metabo2041031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 11/16/2022] Open
Abstract
Specialized compounds from photosynthetic organisms serve as rich resources for drug development. From aspirin to atropine, plant-derived natural products have had a profound impact on human health. Technological advances provide new opportunities to access these natural products in a metabolic context. Here, we describe a database and platform for storing, visualizing and statistically analyzing metabolomics data from fourteen medicinal plant species. The metabolomes and associated transcriptomes (RNAseq) for each plant species, gathered from up to twenty tissue/organ samples that have experienced varied growth conditions and developmental histories, were analyzed in parallel. Three case studies illustrate different ways that the data can be integrally used to generate testable hypotheses concerning the biochemistry, phylogeny and natural product diversity of medicinal plants. Deep metabolomics analysis of Camptotheca acuminata exemplifies how such data can be used to inform metabolic understanding of natural product chemical diversity and begin to formulate hypotheses about their biogenesis. Metabolomics data from Prunella vulgaris, a species that contains a wide range ofantioxidant, antiviral, tumoricidal and anti-inflammatory constituents, provide a case study of obtaining biosystematic and developmental fingerprint information from metabolite accumulation data in a little studied species. Digitalis purpurea, well known as a source of cardiac glycosides, is used to illustrate how integrating metabolomics and transcriptomics data can lead to identification of candidate genes encoding biosynthetic enzymes in the cardiac glycoside pathway. Medicinal Plant Metabolomics Resource (MPM) [1] provides a framework for generating experimentally testable hypotheses about the metabolic networks that lead to the generation of specialized compounds, identifying genes that control their biosynthesis and establishing a basis for modeling metabolism in less studied species. The database is publicly available and can be used by researchers in medicine and plant biology.
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Affiliation(s)
- Eve Syrkin Wurtele
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA.
| | - Joe Chappell
- Department of Cellular and Molecular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - A Daniel Jones
- Department of Biochemistry & Molecular Biology and Deptment of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Mary Dawn Celiz
- Department of Biochemistry & Molecular Biology and Deptment of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Nick Ransom
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA
| | - Ludmila Rizshsky
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011, USA
| | - Matthew Crispin
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA
| | - Philip Dixon
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Jia Liu
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Mark P Widrlechner
- Department of Ecology, Evolution, and Organismal Biology and Department of Horticulture, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Center for Metabolic Biology, The Plant Science Institute, Iowa State University, Ames, IA 50011, USA
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Ko YJ, Moon HW, Hur M, Park CM, Cho SE, Yun YM. Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae in Korean community and hospital settings. Infection 2012; 41:9-13. [PMID: 22723075 DOI: 10.1007/s15010-012-0272-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/24/2012] [Indexed: 11/24/2022]
Abstract
PURPOSE The assessment and early recognition of risk factors for infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are important for infection control and proper treatment. The aim of the present study was to investigate the prevalence of fecal carriage of ESBL-E in healthy individuals and hospitalized high-risk patients in Korea and to compare the characteristics of ESBL-E in these two groups. METHODS A total of 384 samples from 290 healthy individuals and 94 high-risk patients were collected. The screening of ESBL-E was performed using a commercial chromogenic medium. Bacterial identification and antibiotic susceptibility testing were performed using the Vitek 2 system. RESULTS The prevalence of ESBL-E carriage was 20.3 % in healthy individuals and 42.5 % in high-risk patients. Escherichia coli comprised a large majority (96.6 %) of the isolates from healthy individuals, but Klebsiella pneumoniae was more commonly detected (45.0 %) in high-risk patients than in healthy individuals. K. pneumoniae isolates exhibited significantly higher resistance to ceftazidime, ampicillin, and carbapenem, and E. coli exhibited higher resistance to cefotaxime. E. coli from high-risk patients exhibited significantly higher resistance to levofloxacin and cefepime than that from healthy individuals. CONCLUSIONS We demonstrated the high prevalence of ESBL-E carriage in Korea and clarified the characteristics of ESBL-E carriage in healthy individuals and high-risk patients. The distribution and antibiotic susceptibility of colonizing ESBL-E were different between the group of healthy individuals and the high-risk patients. Active surveillance of ESBL-E carriage is suggested for infection control, and the use of chromogenic agar appears to be an efficient method.
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Affiliation(s)
- Y J Ko
- Department of Laboratory Medicine, Konkuk University School of Medicine, Konkuk University Hospital, 4-12, Hwayang-dong, Seoul, 143-729, Korea
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Kang S, Kim S, Kang T, Yoon C, Ko S, Hur M, Lee H, Seol C. 528 Short-term Outcomes of Immediate Breast Reconstruction After Mastectomy Using Implant or Tissue Expander in Patients with Breast Cancer. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)70593-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hur M, Moon HW, Yun YM, Kang TY, Kim HS, Kim HS, Lee KM, Kang SH, Lee EH. Detection of tuberculosis using artus M. tuberculosis PCR Kit and COBAS AMPLICOR Mycobacterium tuberculosis Test. Int J Tuberc Lung Dis 2012; 15:795-8. [PMID: 21575301 DOI: 10.5588/ijtld.10.0367] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Nucleic acid amplification tests can detect Mycobacterium tuberculosis complex rapidly and reliably. OBJECTIVE To compare the diagnostic performance of the artus M. tuberculosis PCR Kit and COBAS AMPLICOR Mycobacterium tuberculosis Test. In the artus assay, an appropriate cycle threshold (Ct) value was determined for positivity. DESIGN A total of 238 clinical respiratory specimens were analysed using both the artus and COBAS AMPLICOR assays. In 221 specimens, these results were further compared with culture results. RESULTS The overall agreement between artus and COBAS AMPLICOR was 96.2% (229/238). Among the nine (3.8%) discrepant specimens, three (1.3%) were artus-positive and COBAS AMPLICOR-negative, while the other six (2.5%) were artus-negative and COBAS AMPLICOR-positive. Using culture as a standard, the sensitivity and specificity of the artus assay were 97.8% and 85.1%, and those of COBAS AMPLICOR assay were 100% and 86.2%, respectively. The difference was not statistically significant. In the artus assay, the minimum Ct value for the positivity determination was 38. CONCLUSION The artus and COBAS AMPLICOR assays showed comparable diagnostic performance and can be confidently used for detection of M. tuberculosis complex. In the artus assay, a Ct value of 38 could be suggested as an appropriate cut-off value.
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Affiliation(s)
- M Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea.
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Moon HW, Hur M, Kim H, Kim JY, Park CM, Yun YM. Isothermal target and probe amplification for Mycobacterium tuberculosis identification from broth cultures. Int J Tuberc Lung Dis 2012; 16:516-20. [PMID: 22325060 DOI: 10.5588/ijtld.11.0220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Various methods are used to identify Mycobacterium tuberculosis complex (MTC) from broth cultures. The isothermal target and probe amplification (iTPA) method has recently been introduced as a simple and cost-effective molecular assay. OBJECTIVE To evaluate the diagnostic performance of the iTPA method. DESIGN A total of 175 specimens from the Mycobacteria Growth Indicator Tube (MGIT) 960 broth culture system were evaluated. The immunochromatographic test (ICT) and real-time quantitative PCR (RQ-PCR) were compared with the iTPA method. RESULTS MTC was identified in 71/131 MGIT-positive specimens, including 60 ICT-positive and 11 ICT- negative/PCR-positive specimens. The sensitivity and specificity of the ICT assay were respectively 84.5% (95%CI 74.0-92.0) and 100% (95%CI 94.0-100). These 71 specimens were all MTC-positive with the iTPA method also. Sixty non-tuberculous mycobacteria specimens and 44 MGIT-negative specimens were all MTC-negative with the iTPA method. CONCLUSION Our data show that the diagnostic performance of the iTPA method is comparable to that of RQ-PCR. The iTPA method could be a reliable and cost-effective option for the identification of MTC from broth culture.
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Affiliation(s)
- H-W Moon
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
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Hur M, Yeo I, Park E, Kim YH, Yoo J, Kim E, No MH, Koh J, Kim S. Combination of Statistical Methods and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for More Comprehensive, Molecular-Level Interpretations of Petroleum Samples. Anal Chem 2009; 82:211-8. [DOI: 10.1021/ac901748c] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manhoi Hur
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Injoon Yeo
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Eunsuk Park
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Young Hwan Kim
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Jongshin Yoo
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Eunkyoung Kim
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Myoung-han No
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Jaesuk Koh
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Sunghwan Kim
- Department of Bioinformatics, Korea University, Seoul, Korea, Mass Spectrometry Group, Korean Basic Science Institute, Mass Spectrometry Team, Ochang, Korea, SK Energy Institute of Technology, Daejeon, Korea, and Department of Chemistry, Kyungpook National University, Daegu, Korea
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Moon HW, Noh JK, Hur M, Yun YM, Lee CH, Kwon SY. High prevalence of autoantibodies in hepatitis A infection: the impact on laboratory profiles. J Clin Pathol 2009; 62:786-8. [DOI: 10.1136/jcp.2009.064410] [Citation(s) in RCA: 11] [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] [Indexed: 11/04/2022]
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