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Chen K, Alexander LE, Mahgoub U, Okazaki Y, Higashi Y, Perera AM, Showman LJ, Loneman D, Dennison TS, Lopez M, Claussen R, Peddicord L, Saito K, Lauter N, Dorman KS, Nikolau BJ, Yandeau-Nelson MD. Dynamic relationships among pathways producing hydrocarbons and fatty acids of maize silk cuticular waxes. PLANT PHYSIOLOGY 2024; 195:2234-2255. [PMID: 38537616 PMCID: PMC11213258 DOI: 10.1093/plphys/kiae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 06/30/2024]
Abstract
The hydrophobic cuticle is the first line of defense between aerial portions of plants and the external environment. On maize (Zea mays L.) silks, the cuticular cutin matrix is infused with cuticular waxes, consisting of a homologous series of very long-chain fatty acids (VLCFAs), aldehydes, and hydrocarbons. Together with VLC fatty-acyl-CoAs (VLCFA-CoAs), these metabolites serve as precursors, intermediates, and end-products of the cuticular wax biosynthetic pathway. To deconvolute the potentially confounding impacts of the change in silk microenvironment and silk development on this pathway, we profiled cuticular waxes on the silks of the inbreds B73 and Mo17, and their reciprocal hybrids. Multivariate interrogation of these metabolite abundance data demonstrates that VLCFA-CoAs and total free VLCFAs are positively correlated with the cuticular wax metabolome, and this metabolome is primarily affected by changes in the silk microenvironment and plant genotype. Moreover, the genotype effect on the pathway explains the increased accumulation of cuticular hydrocarbons with a concomitant reduction in cuticular VLCFA accumulation on B73 silks, suggesting that the conversion of VLCFA-CoAs to hydrocarbons is more effective in B73 than Mo17. Statistical modeling of the ratios between cuticular hydrocarbons and cuticular VLCFAs reveals a significant role of precursor chain length in determining this ratio. This study establishes the complexity of the product-precursor relationships within the silk cuticular wax-producing network by dissecting both the impact of genotype and the allocation of VLCFA-CoA precursors to different biological processes and demonstrates that longer chain VLCFA-CoAs are preferentially utilized for hydrocarbon biosynthesis.
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Affiliation(s)
- Keting Chen
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Liza E Alexander
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Umnia Mahgoub
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Yozo Okazaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Yasuhiro Higashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ann M Perera
- W.M. Keck Metabolomics Research Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Lucas J Showman
- W.M. Keck Metabolomics Research Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Derek Loneman
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Tesia S Dennison
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Miriam Lopez
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Reid Claussen
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Layton Peddicord
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Nick Lauter
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Karin S Dorman
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Marna D Yandeau-Nelson
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA
- Interdepartmental Genetics & Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
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Will I, Attardo GM, de Bekker C. Multiomic interpretation of fungus-infected ant metabolomes during manipulated summit disease. Sci Rep 2023; 13:14363. [PMID: 37658067 PMCID: PMC10474057 DOI: 10.1038/s41598-023-40065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023] Open
Abstract
Camponotus floridanus ants show altered behaviors followed by a fatal summiting phenotype when infected with manipulating Ophiocordyceps camponoti-floridani fungi. Host summiting as a strategy to increase transmission is also observed with parasite taxa beyond fungi, including aquatic and terrestrial helminths and baculoviruses. The drastic phenotypic changes can sometimes reflect significant molecular changes in gene expression and metabolite concentrations measured in manipulated hosts. Nevertheless, the underlying mechanisms still need to be fully characterized. To investigate the small molecules producing summiting behavior, we infected C. floridanus ants with O. camponoti-floridani and sampled their heads for LC-MS/MS when we observed the characteristic summiting phenotype. We link this metabolomic data with our previous genomic and transcriptomic data to propose mechanisms that underlie manipulated summiting behavior in "zombie ants." This "multiomic" evidence points toward the dysregulation of neurotransmitter levels and neuronal signaling. We propose that these processes are altered during infection and manipulation based on (1) differential expression of neurotransmitter synthesis and receptor genes, (2) altered abundance of metabolites and neurotransmitters (or their precursors) with known behavioral effects in ants and other insects, and (3) possible suppression of a connected immunity pathway. We additionally report signals for metabolic activity during manipulation related to primary metabolism, detoxification, and anti-stress protectants. Taken together, these findings suggest that host manipulation is likely a multi-faceted phenomenon, with key processes changing at multiple levels of molecular organization.
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Affiliation(s)
- I Will
- Biology Department, University of Central Florida, Orlando, USA.
| | - G M Attardo
- Entomology and Nematology Department, University of California-Davis, Davis, USA
| | - C de Bekker
- Biology Department, University of Central Florida, Orlando, USA.
- Biology Department, Utrecht University, Utrecht, The Netherlands.
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Bornhofen E, Fè D, Nagy I, Lenk I, Greve M, Didion T, Jensen CS, Asp T, Janss L. Genetic architecture of inter-specific and -generic grass hybrids by network analysis on multi-omics data. BMC Genomics 2023; 24:213. [PMID: 37095447 PMCID: PMC10127077 DOI: 10.1186/s12864-023-09292-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/02/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Understanding the mechanisms underlining forage production and its biomass nutritive quality at the omics level is crucial for boosting the output of high-quality dry matter per unit of land. Despite the advent of multiple omics integration for the study of biological systems in major crops, investigations on forage species are still scarce. RESULTS Our results identified substantial changes in gene co-expression and metabolite-metabolite network topologies as a result of genetic perturbation by hybridizing L. perenne with another species within the genus (L. multiflorum) relative to across genera (F. pratensis). However, conserved hub genes and hub metabolomic features were detected between pedigree classes, some of which were highly heritable and displayed one or more significant edges with agronomic traits in a weighted omics-phenotype network. In spite of tagging relevant biological molecules as, for example, the light-induced rice 1 (LIR1), hub features were not necessarily better explanatory variables for omics-assisted prediction than features stochastically sampled and all available regressors. CONCLUSIONS The utilization of computational techniques for the reconstruction of co-expression networks facilitates the identification of key omic features that serve as central nodes and demonstrate correlation with the manifestation of observed traits. Our results also indicate a robust association between early multi-omic traits measured in a greenhouse setting and phenotypic traits evaluated under field conditions.
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Affiliation(s)
- Elesandro Bornhofen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
| | - Dario Fè
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Morten Greve
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
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Zhu YM, Dong JJ, Jin J, Liu JH, Zheng XQ, Lu JL, Liang YR, Ye JH. Roasting process shaping the chemical profile of roasted green tea and the association with aroma features. Food Chem 2021; 353:129428. [PMID: 33714119 DOI: 10.1016/j.foodchem.2021.129428] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/31/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022]
Abstract
Roasting process impacts the chemical profile and aroma of roasted tea. To compare the impacts of far-infrared irradiation and drum roasting treatments (light, medium and heavy degrees), the corresponding roasted teas were prepared from steamed green tea for chemical analyses and quantitative descriptive analysis on aroma, and correlations between volatiles and aroma attributes were studied. There were 8 catechins, 13 flavonol glycosides and 105 volatiles quantified. Under heavy roasting treatments, most catechins and flavonol glycosides decreased, and aldehydes, ketones, furans, pyrroles/pyrazines, and miscellaneous greatly increased, while far-infrared irradiated teas had distinct nutty aroma compared with the roasty and burnt odor of drum roasted teas. The weighted correlation network analysis result showed that 56 volatiles were closely correlated with the aroma attributes of roasted teas. This study reveals the differential chemical and sensory changes of roasted teas caused by different roasting processes, and provides a novel way for flavor chemistry study.
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Affiliation(s)
- Yu-Meng Zhu
- Zhejiang University Tea Research Institute, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jun-Jie Dong
- Zhejiang Camel Transworld (Organic Food) Co., Ltd., 16 Chachang Road, Yuhang District, Hangzhou 310000, China
| | - Jing Jin
- Zhejiang Agricultural Technical Extension Center, 29 Fengqidong Road, Hangzhou 310000, China
| | - Jin-Hua Liu
- Zhejiang Camel Transworld (Organic Food) Co., Ltd., 16 Chachang Road, Yuhang District, Hangzhou 310000, China
| | - Xin-Qiang Zheng
- Zhejiang University Tea Research Institute, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jian-Liang Lu
- Zhejiang University Tea Research Institute, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yue-Rong Liang
- Zhejiang University Tea Research Institute, 866 Yuhangtang Road, Hangzhou 310058, China.
| | - Jian-Hui Ye
- Zhejiang University Tea Research Institute, 866 Yuhangtang Road, Hangzhou 310058, China.
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Vignoli A, Tenori L, Luchinat C, Saccenti E. Differential Network Analysis Reveals Molecular Determinants Associated with Blood Pressure and Heart Rate in Healthy Subjects. J Proteome Res 2020; 20:1040-1051. [PMID: 33274633 PMCID: PMC7786375 DOI: 10.1021/acs.jproteome.0c00882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
There
is mounting evidence that subclinical
nonpathological high blood pressure and heart rate during youth and
adulthood steadily increase the risk of developing a cardiovascular
disease at a later stage. For this reason, it is important to understand
the mechanisms underlying the subclinical elevation of blood pressure
and heart rate in healthy, relatively young individuals. In the present
study, we present a network-based metabolomic study of blood plasma
metabolites and lipids measured using nuclear magnetic resonance spectroscopy
on 841 adult healthy blood donor volunteers, which were stratified
for subclinical low and high blood pressure (systolic and diastolic)
and heart rate. Our results indicate a rewiring of metabolic pathways
active in high and low groups, indicating that the subjects with subclinical
high blood pressure and heart rate could present latent cardiometabolic
dysregulations.
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Affiliation(s)
- Alessia Vignoli
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
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Behrouzi P, Grootswagers P, Keizer PLC, Smeets ETHC, Feskens EJM, de Groot LCPGM, van Eeuwijk FA. Dietary Intakes of Vegetable Protein, Folate, and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models. J Nutr 2020; 150:634-643. [PMID: 31858107 PMCID: PMC7056616 DOI: 10.1093/jn/nxz269] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/14/2019] [Accepted: 10/09/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND In nutritional epidemiology, dealing with confounding and complex internutrient relations are major challenges. An often-used approach is dietary pattern analyses, such as principal component analysis, to deal with internutrient correlations, and to more closely resemble the true way nutrients are consumed. However, despite these improvements, these approaches still require subjective decisions in the preselection of food groups. Moreover, they do not make efficient use of multivariate dietary data, because they detect only marginal associations. We propose the use of copula graphical models (CGMs) to model and make statistical inferences regarding complex associations among variables in multivariate data, where associations between all variables can be learned simultaneously. OBJECTIVE We aimed to reconstruct nutritional intake and physical functioning networks in Dutch older adults by applying a CGM. METHODS We addressed this issue by uncovering the pairwise associations between variables while correcting for the effect of remaining variables. More specifically, we used a CGM to infer the precision matrix, which contains all the conditional independence relations between nodes in the graph. The nonzero elements of the precision matrix indicate the presence of a direct association. We applied this method to reconstruct nutrient-physical functioning networks from the combined data of 4 studies (Nu-Age, ProMuscle, ProMO, and V-Fit, total n = 662, mean ± SD age = 75 ± 7 y). The method was implemented in the R package nutriNetwork which is freely available at https://cran.r-project.org/web/packages/nutriNetwork. RESULTS Greater intakes of vegetable protein and vitamin B-6 were partially correlated with higher scores on the total Short Physical Performance Battery (SPPB) and the chair rise test. Greater intakes of vitamin B-12 and folate were partially correlated with higher scores on the chair rise test and the total SPPB, respectively. CONCLUSIONS We determined that vegetable protein, vitamin B-6, folate, and vitamin B-12 intakes are partially correlated with improved functional outcome measurements in Dutch older adults.
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Affiliation(s)
- Pariya Behrouzi
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, Wageningen, Netherlands
| | - Pol Grootswagers
- Department of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands
| | - Paul L C Keizer
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, Wageningen, Netherlands
| | - Ellen T H C Smeets
- Department of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands
| | - Edith J M Feskens
- Department of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands
| | | | - Fred A van Eeuwijk
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, Wageningen, Netherlands
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