Accessing the natural variation of the abundances of major lignans in the heartwood of Taiwania cryptomerioides by 1H-NMR and LC-MS profiling

Abstract Lignans are major bioactive secondary metabolites, which are also formed in the heartwood (hW) of Taiwania (Taiwania cryptomerioides). Their biosynthesis pathways are complex and involve many enzymes and intermediates. To evaluate the extent of the genetic components leading to the variety of lignans in Taiwania hW, 35 Taiwania genotypes of four provenances were surveyed using the proton nuclear magnetic resonance (1H-NMR) and liquid chromatography-mass spectrometry (LC-MS) analyses. The metabolite profiles were statistically evaluated by principal component analysis (PCA) and the general linear model (GLM). The broad-sense heritability (H2) was further evaluated by linear mixed model (LMM) analysis. It was demonstrated that the genetic factor is the major contributor to the abundance of lignans, though the environmental factor also has some effect on it. Among the metabolites detected by 1H-NMR, lignans were the major compounds that exhibited high a H2 (0.52–0.82), which was further verified by LC-MS. The conclusion is that 1H-NMR spectroscopy is suitable for quick screenings, predictions and semi-quantitation of lignans. The high H2 is also indicative of the lignan abundances as traits that can be genetically modified to achieve a significant wood quality improvement.

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Differences in the metabolite profiles of tender leaves of wheat, barley, rye and Triticale based on LC-MS

10.1101/2020.12.03.409847 ◽

2020 ◽

Author(s):

Piyi Xing ◽

Zhenqiao Song ◽

Xingfeng Li

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Principal Component ◽

Liquid Chromatography Mass Spectrometry ◽

Metabolomics Data ◽

Chromatography Mass Spectrometry ◽

Metabolite Profiles ◽

Positive Mode ◽

Sugar Derivatives ◽

Important Basis

AbstractWheatgrass has emerged as a functional food source in recent years, but the detailed metabolomics basis for its health benefits remains poorly understood. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis were used to study the metabolic profiling of seedlings from wheat, barley, rye and triticale, which revealed 1800 features in positive mode and 4303 features in negative mode. Principal component analysis (PCA) showed clear differences between species, and 164 differentially expressed metabolites (DEMs) were detected, including amino acids, organic acids, lipids, fatty acids, nucleic acids, flavonoids, amines, polyamines, vitamins, sugar derivatives and others. Unique metabolites in each species were identified. This study provides a glimpse into the metabolomics profiles of wheat and its wild relatives, which may form an important basis for nutrition, health and other parameters.Practical ApplicationThis manuscript present liquid chromatography-mass spectrometry (LC-MS) results of young sprouts of common wheat and its relatives. Our results may help to better understand the natural variation due to the genotype before metabolomics data are considered for application to wheatgrass and can provide a basis (assessment) for its potential pharmaceutical and nutritional value.

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Effect of Saffron Extract and Crocin in Serum Metabolites of Induced Obesity Rats

BioMed Research International ◽

10.1155/2020/1247946 ◽

2020 ◽

Vol 2020 ◽

pp. 1-15

Author(s):

Fatin Najwa Ramli ◽

Azliana Abu Bakar Sajak ◽

Faridah Abas ◽

Zulfitri Azuan Mat Daud ◽

Azrina Azlan

Keyword(s):

High Fat Diet ◽

Crocus Sativus ◽

Proton Nuclear Magnetic Resonance ◽

High Fat ◽

H Nmr ◽

Metabolite Profiles ◽

Obese Rats ◽

Saffron Extract ◽

Primary Compound ◽

Different Doses

The effect of saffron extract (Crocus sativus L.) and its primary compound crocin was studied on an induced obesity rat model. Our study is aimed at investigating and comparing the metabolite changes in obese and obese treated with saffron extract and crocin and at improving the understanding of the therapeutic effect of saffron extract and crocin. Two different doses of saffron extracts and crocin (40 and 80 mg/kg) were incorporated in a high-fat diet (HFD) and were given for eight weeks to the obese rats. The changes in metabolite profiles of the serum were determined using proton nuclear magnetic resonance (1H-NMR). Pattern recognition by multivariate data analysis (MVDA) showed that saffron extract and crocin at 80 mg/kg was the best dosage compared to 40 mg/kg. It also showed that both treatments work in different pathways, especially concerning glucose, lipid, and creatinine metabolism. In conclusion, although the pure compound, crocin, is superior to the saffron crude extract, this finding suggested that the saffron extract can be considered as an alternative aside from crocin in treating obesity.

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Tree Growth and Wood Quality in Pure Vs. Mixed-Species Stands of European Beech and Calabrian Pine in Mediterranean Mountain Forests

Forests ◽

10.3390/f11010006 ◽

2019 ◽

Vol 11 (1) ◽

pp. 6 ◽

Cited By ~ 3

Author(s):

Diego Russo ◽

Pasquale A. Marziliano ◽

Giorgio Macrì ◽

Giuseppe Zimbalatti ◽

Roberto Tognetti ◽

...

Keyword(s):

Tree Growth ◽

Mixed Model ◽

Linear Mixed Model ◽

Wood Quality ◽

European Beech ◽

Growth Patterns ◽

Mixed Species ◽

Area Index ◽

Mixture Effect ◽

Calabrian Pine

Mixed-species forests may deliver more forest functions and services than monocultures, as being considered more resistant to disturbances than pure stands. However, information on wood quality in mixed-species vs. corresponding pure forests is poor. In this study, nine plots grouped into three triplets of pure and mixed-species stands of European beech and Calabrian pine (three dominated by European beech, three dominated by Calabrian pine, and three mixed-species plots) were analysed. We evaluated tree growth and wood quality through dendrochronological approaches and non-destructive technologies (acoustic detection), respectively, hypothesizing that the mixture might improve the fitness of each species and its wood quality. A linear mixed model was applied to test the effects of exogenous influences on the basal area index (BAI) and the dynamic modulus of elasticity (MOEd). The recruitment period (Rp) was studied to verify whether wood quality was independent from stem radial growth patterns. Results showed that the mixture effect influenced both wood quality and BAI. In the mixed-species plots, for each species, MOEd values were significantly higher than in the corresponding pure stands. The mixture effect aligned MOEd values, making wood quality uniform across the different diameter classes. In the mixed-species plots, a significant positive relationship between MOEd and Rp, but also significantly higher BAI values than in the pure plots, were found for European beech, but not for Calabrian pine. The results suggest the promotion of mixing of European beech and Calabrian pine in this harsh environment to potentially improve both tree growth and wood quality.

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Principal Component Regression and Linear Mixed Model in Association Analysis of Structured Samples: Competitors or Complements?

Genetic Epidemiology ◽

10.1002/gepi.21879 ◽

2014 ◽

Vol 39 (3) ◽

pp. 149-155 ◽

Cited By ~ 12

Author(s):

Yiwei Zhang ◽

Wei Pan

Keyword(s):

Association Analysis ◽

Mixed Model ◽

Linear Mixed Model ◽

Principal Component Regression ◽

Principal Component

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Stability of Rice Mutant Lines By Linear Mixed Model And Suggestion A New Index Based For Yield Performance And Stability

10.21203/rs.3.rs-895572/v1 ◽

2021 ◽

Author(s):

Peyman Sharifi ◽

Ali Akbar Ebadi ◽

Mohammad Taher Hallajian

Keyword(s):

Mixed Model ◽

Linear Mixed Model ◽

Block Design ◽

Weighted Average ◽

Principal Component ◽

Fars Province ◽

Yield Performance ◽

Rice Mutant ◽

Superior Genotypes ◽

Mutant Lines

Abstract Fourteen rice mutant lines with four cultivars were evaluated in a randomized complete block design with three replications in three locations in Iran (Rasht, ChaparSar and Fars province) during two growing seasons (2014-2016). In addition, a new index namely as equivalent index of stability and performance (EISP) is suggested for simultaneous evaluation of yield performance and stability. The heat map of yield performance and WAASB (weighted average of absolute scores based on BLUP (best linear unbiased prediction)) identified G3, G9, G6, G12 and G5 as highly productive and stable genotypes. Based on the analysis by multi-trait stability index (MTSI) G7, G5 and G1 were selected as superior genotypes. The top five superior genotypes based on harmonic mean and of the relative performance of genotypic values (HMRPGV) were G5, G12, G7, G2 and G1. For verification of EISP, its value was calculated for some of multi and univariate stability indices and identified genotypes G5 and G12 as the best ones. Principal component analysis indicated yield positively correlated with HMGV, RPGV, HMRPGV, EIS2P EIbP and EIPiP. In conclusion, G12, G5 and G9 had a significant advantage over all genotypes and could undergo selection or cultivar introduction processes.

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Secondary Genome-Wide Association Study Using Novel Analytical Strategies Disentangle Genetic Components of Cleft Lip and/or Cleft Palate in 1q32.2

Genes ◽

10.3390/genes11111280 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1280

Author(s):

Yunju Yang ◽

Akiko Suzuki ◽

Junichi Iwata ◽

Goo Jun

Keyword(s):

Association Study ◽

Cleft Lip ◽

Mixed Model ◽

Linear Mixed Model ◽

Genome Wide Association Study ◽

P Value ◽

Genetic Components ◽

Genome Wide ◽

Analytical Strategies ◽

Project Data

Orofacial cleft (OFC) is one of the most prevalent birth defects, leading to substantial and long-term burdens in a newborn’s quality of life. Although studies revealed several genetic variants associated with the birth defect, novel approaches may provide additional clues about its etiology. Using the Center for Craniofacial and Dental Genetics project data (n = 10,542), we performed linear mixed-model analyses to study the genetic compositions of OFC and investigated the dependence among identified loci using conditional analyses. To identify genes associated with OFC, we conducted a transcriptome-wide association study (TWAS) based on predicted expression levels. In addition to confirming the previous findings at four loci, 1q32.2, 8q24, 2p24.2 and 17p13.1, we untwined two independent loci at 1q32.2, TRAF3IP3 and IRF6. The sentinel SNP in TRAF3IP3 (rs2235370, p-value = 5.15 × 10−9) was independent of the sentinel SNP at IRF6 (rs2235373, r2 < 0.3). We found that the IRF6 effect became nonsignificant once the 8q24 effect was conditioned, while the TRAF3IP3 effect remained significant. Furthermore, we identified nine genes associated with OFC in TWAS, implicating a glutathione synthesis and drug detoxification pathway. We identified some meaningful additions to the OFC etiology using novel statistical methods in the existing data.

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Genomic regions associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep

10.1101/2021.02.04.429710 ◽

2021 ◽

Author(s):

Michelle R. Mousel ◽

Stephen N. White ◽

Maria K. Herndon ◽

David R. Herndon ◽

J. Bret Taylor ◽

...

Keyword(s):

Copy Number ◽

Mixed Model ◽

Principal Component ◽

Production Cycle ◽

Domestic Sheep ◽

Dna Copy Number ◽

Immune Genes ◽

Genetic Components ◽

Genome Wide ◽

Mycoplasma Ovipneumoniae

AbstractMycoplasma ovipneumoniae contributes to polymicrobial pneumonia in domestic sheep. Elucidation of host genetic components to M. ovipneumoniae nasal detection would have the potential to reduce the incidence of pneumonia. Nasal mucosal secretions were collected from 647 sheep from a large US sheep flock. Ewes of three breeds (Polypay n=222, Rambouillet n=321, and Suffolk n=104) ranging in age from one to seven years, were sampled at three different times of the production cycle (February, April, and September/October) over four years (2015 to 2018). The presence and quantity of M. ovipneumoniae was determined using a species-specific qPCR with 3 to 10 sampling times per sheep. Breed (P<0.001), age (P<0.024), sampling time (P<0.001), and year (P<0.001) of collection affected log10 transformed M. ovipneumoniae DNA copy number, where Rambouillet had the lowest (P<0.0001) compared with both Polypay and Suffolk demonstrating a possible genetic component to detection. Samples from yearlings, April, and 2018 had the highest (P<0.046) detected DNA copy number mean. Sheep genomic DNA was genotyped with the Illumina OvineHD BeadChip. Principal component analysis identified most of the variation in the dataset was associated with breed. Therefore, genome wide association analysis was conducted with a mixed model (EMMAX), with principle components 1 to 6 as fixed and a kinship matrix as random effects. Genome-wide significant (P<9×10−8) SNPs were identified on chromosomes 6 and 7 in the all-breed analysis. Individual breed analysis had genome-wide significant (P<9×10−8) SNPs on chromosomes 3, 4, 7, 9, 10, 15, 17, and 22. Annotated genes near these SNPs are part of immune (ANAPC7, CUL5, TMEM229B, PTPN13), gene translation (PIWIL4), and chromatin organization (KDM2B) pathways. Immune genes are expected to have increased expression when leukocytes encounter M. ovipneumoniae which would lead to chromatin reorganization. Work is underway to narrow the range of these associated regions to identify the underlying causal mutations.

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Metabolite Profiles of Red and Yellow Watermelon (Citrullus lanatus) Cultivars Using a 1H-NMR Metabolomics Approach

Molecules ◽

10.3390/molecules25143235 ◽

2020 ◽

Vol 25 (14) ◽

pp. 3235 ◽

Cited By ~ 1

Author(s):

Fadzil Sulaiman ◽

Amalina Ahmad Azam ◽

Muhammad Safwan Ahamad Bustamam ◽

Sharida Fakurazi ◽

Faridah Abas ◽

...

Keyword(s):

1H Nmr ◽

Deuterium Oxide ◽

Citrullus Lanatus ◽

Principal Component ◽

Solvent System ◽

Proton Nuclear Magnetic Resonance ◽

Metabolite Profiles ◽

Polar Metabolites ◽

Distinct Color ◽

Β Carotene

Watermelon, a widely commercialized fruit, is famous for its thirst-quenching property. The broad range of cultivars, which give rise to distinct color and taste, can be attributed to the differences in their chemical profile, especially that of the carotenoids and volatile compounds. In order to understand this distribution properly, water extracts of red and yellow watermelon pulps with predominantly polar metabolites were subjected to proton nuclear magnetic resonance (1H-NMR) analysis. Deuterium oxide (D2O) and deuterated chloroform (CDCl3) solvents were used to capture both polar and non-polar metabolites from the same sample. Thirty-six metabolites, of which six are carotenoids, were identified from the extracts. The clustering of the compounds was determined using unsupervised principal component analysis (PCA) and further grouping was achieved using supervised orthogonal partial least squares discriminant analysis (OPLS-DA). The presence of lycopene, β-carotene, lutein, and prolycopene in the red watermelon plays an important role in its differentiation from the yellow cultivar. A marked difference in metabolite distribution was observed between the NMR solvents used as evidenced from the PCA model. OPLS-DA and relative quantification of the metabolites, on the other hand, helped in uncovering the discriminating metabolites of the red and yellow watermelon cultivars from the same solvent system.

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Background ozone over Canada and the United States

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-9-21111-2009 ◽

2009 ◽

Vol 9 (5) ◽

pp. 21111-21164 ◽

Cited By ~ 1

Author(s):

E. Chan ◽

R. J. Vet

Keyword(s):

United States ◽

Mixed Model ◽

Linear Mixed Model ◽

Principal Component ◽

The United States ◽

Eastern Canada ◽

Mixing Ratios ◽

Background Ozone ◽

The Pacific ◽

Decadal Scale

Abstract. Planetary boundary layer (PBL) ozone temporal variations were investigated on diurnal, seasonal and decadal scales in various regions across Canada and the United States for the period 1997–2006. Background ozone is difficult to quantify and define through observations. In light of the importance of its estimates for achievable policy targets, evaluation of health impacts and relationship with climate, background ozone mixing ratios were estimated. Principal Component Analyses (PCA) were performed using 97 non-urban ozone sites for each season to define contiguous regions. Backward air parcel trajectories were used to systematically select the cleanest background air cluster associated with the lowest May–September 95th percentile for each site. Decadal ozone trends were estimated by season for each PCA-derived region using a~generalized linear mixed model (GLMM). Background ozone mixing ratios were variable geographically and seasonally. For example, the mixing ratios annually ranged from 21 to 38, and 23 to 38 ppb for the continental Eastern Canada and Eastern US. The Pacific and Atlantic coastal regions typically had relatively low background levels ranging from 14 to 24, and 17 to 36 ppb, respectively. On the decadal scale, the direction and magnitude of trends are different in all seasons across the regions (−1.56 to +0.93 ppb/a). Trends increased in the Pacific region for all seasons. Background ozone decadal changes are shown to be masked by the much stronger regional signals in areas that have seen substantial reductions of ozone precursors since the early 2000s.

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Metabolite Profiling of Three Curcuma Species (Zingiberaceae) Based on H-NMR Spectroscopy

ALCHEMY Jurnal Penelitian Kimia ◽

10.20961/alchemy.15.1.23914.79-88 ◽

2019 ◽

Vol 15 (1) ◽

pp. 79

Author(s):

Dinar Sari Cahyaningrum Wahyuni ◽

Mutya Puti Wardianti ◽

Yudi Rinanto ◽

Soerya Dewi Marliyana

Keyword(s):

Nmr Spectroscopy ◽

Secondary Metabolites ◽

Curcuma Longa ◽

Quantitative Characteristic ◽

Principal Component ◽

Proton Nuclear Magnetic Resonance ◽

Tropical Region ◽

Anticancer Activities ◽

Primary And Secondary Metabolites ◽

H Nmr

Genus Curcuma, Zingiberaceae, is a typical medicinal plant in tropical region especially in Indonesia. It has been studied to have antioxidant, antimicrobial, antitumor, anti-inflammatory and anticancer activities. However, little knowledge of the metabolic profile both primary and secondary metabolites have been reported. Thus, this study aims to investigate metabolic profiling both primary and secondary metabolites simultaneously in the Curcuma species based on proton nuclear magnetic resonance (1H-NMR) spectroscopy. The present work applied metabolomic study which measured the qualitative and quantitative characteristic metabolites. The Curcuma species, Curcuma aeruginosa Roxb., Curcuma xanthorrhiza Roxb., and Curcuma longa L., collected from Nguter, Sukoharjo, Indonesia. Two-dimensional (2D)-NMR techniques were applied to further identify a number of different types of compounds. Multivariate data analysis such as Principal Component Analysis (PCA) applied to reveal differences among species. A clear difference occurred among 3 Curcuma species. Primary metabolites responsible for the discrimination are alanine (C. xanthorrhiza Roxb. was 3.78 times higher than in C. longa L), sugars (C. xanthorrhiza Roxb. were 6.03 and 3.81 times higher in C. aeruginosa Roxb. and C. longa L. respectively). Besides, secondary metabolites which differed among 3 species are curcumin (C. xanthorrhiza Roxb. were 38.25 and 25 times higher than in C. aeruginosa Roxb.) and xanthorrhizol (C. longa L. were 62 and 44.4 times higher than in C aeruginosa Roxb.).

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