scholarly journals Mining the Wheat Grain Proteome

2022 ◽  
Vol 23 (2) ◽  
pp. 713
Author(s):  
Delphine Vincent ◽  
AnhDuyen Bui ◽  
Doris Ram ◽  
Vilnis Ezernieks ◽  
Frank Bedon ◽  
...  
Keyword(s):  
Guanidine Hydrochloride ◽  
Internal Standard ◽  
Independent Set ◽  
Breeding Cycle ◽  
Breeding Lines ◽  
Mapping Tool ◽  
Feed Source ◽  
Screening Assays ◽  
Grain Proteome ◽  
Best Parameters

Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).

scholarly journals Improvement of Genomic Prediction in Advanced Wheat Breeding Lines by Including Additive × additive Epistasis

2021 ◽  
Author(s):  
Miguel Angel Raffo ◽  
Pernille Sarup ◽  
Xiangyu Guo ◽  
Huiming Liu ◽  
Jeppe Reitan Andersen ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Cross Validation ◽  
Best Linear Unbiased Prediction ◽  
Wheat Breeding ◽  
Breeding Cycle ◽  
Linear Unbiased Prediction ◽  
Breeding Lines ◽  
Genetic Merit ◽  
Best Linear Unbiased ◽  
Unbiased Prediction

Abstract Epistasis is the principal non-additive genetic effect in inbred wheat lines and can be used to develop cultivars based on total genetic merit. Correct models for variance components (VCs) estimation are needed to disentangle the genetic architecture of complex traits in wheat. We aimed to i) evaluate the performance of extended genomic best linear unbiased prediction (EG-BLUP) and the natural and orthogonal interactions approach (NOIA) for VCs estimation in a commercial wheat-breeding population, and ii) investigate whether including epistasis in genomic prediction enhance predictive ability (PA) for wheat breeding lines. In total, 2,060 sixth-generation (F6) lines from Nordic Seed A/S breeding company were phenotyped for grain yield over 21-year-x-location combinations in Denmark, and genotyped using 15K Illumina-BeadChip. Four models were used to estimate VCs and heritability at plot level: i) Baseline, ii) Genomic best linear unbiased prediction (G-BLUP), iii) EG-BLUP, and iv) NOIA. Narrow- and broad-sense heritabilities estimated with G-BLUP were 0.15 and 0.31, respectively. EG-BLUP and NOIA failed to achieve orthogonal partition of genetic variances. Even though NOIA removed Hardy-Weinberg equilibrium assumption, both models yielded very similar estimates, indicating that linkage disequilibrium causes the lack of orthogonality. The PA was studied using leave-one-line-out and leave-one-breeding-cycle-out cross-validations. Both EG-BLUP and NOIA increased PA significantly (16.5%) compared to G-BLUP in leave-one-line-out cross-validation. However, the improvement for including epistasis was not observed in the leave-one-breeding-cycle-out cross-validation. We conclude that although the variance partition into orthogonal genetic effects was not possible, epistatic models can be useful to enhance predictions of total genetic merit.

Improved staining characteristics of serum lipids after halogenation and esterification of thin-layer chromatograms.

1977 ◽  
Vol 23 (5) ◽  
pp. 835-841 ◽  
Author(s):  
W R Nelson ◽  
S Natelson
Keyword(s):  
Fatty Acids ◽  
Thin Layer ◽  
Free Fatty Acids ◽  
Free Cholesterol ◽  
Relative Concentration ◽  
Guanidine Hydrochloride ◽  
Internal Standard ◽  
Double Bonds ◽  
Erythrosine B ◽  
Iodine Monobromide

Abstract We describe a procedure for treatment of thin-layer chromatographic serum lipid patterns so that they may be stained by dyes for evaluation by densitometry. After development of the chromatogram [Clin. Chem. 18, 384 (1972)] the plates are dried and sprayed with butyryl chloride. This esterifies the free cholesterol. After drying, the plate is treated with iodine monobromide, to add iodline to the double bonds. The triacylglycerols (triglycerides), cholesterol esters, free cholesterol, and phospholipids are now all in the form of esters with no unsaturated double bonds. The free fatty acids are also now saturated. The chromatogram is now stained with basic fuchsine in acetate buffer (0.1 mol/liter, pH 5.0). Excess stain is removed with a buffered solution of guanidine hydrochloride. Erythrosine B may also be used. With basic fuchsine the background will be a uniform pink. With erythrosine B the background is white, but the stain tends to be washed out of the free fatty acids. The chromatograms are evaluated by densitometry, with use of a 540-nm filter for basic fuchsine and a 520-nm filter for erythrosine B. The stained chromatograms and densitometric scans accurately represent the relative concentration of the various lipid fractions as compared to that of an internal standard, and correlate with the nature of the disease being explored.

scholarly journals Rapid Quantification of Ethyl Carbamate in Spirits Using NMR Spectroscopy and Chemometrics

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Yulia B. Monakhova ◽  
Thomas Kuballa ◽  
Dirk W. Lachenmeier
Keyword(s):  
Nmr Spectroscopy ◽  
Internal Standard ◽  
Independent Set ◽  
Ethyl Carbamate ◽  
Fermented Food ◽  
Alcoholic Beverages ◽  
Sample Extraction ◽  
Sensitivity And Selectivity ◽  
First Time ◽  
Fruit Spirits

Ethyl carbamate (EC, urethane, C2H5OCONH2) is a genotoxic carcinogen and is regularly found in fermented food products including alcoholic beverages. In this study, the rapid method of nuclear magnetic resonance (NMR) spectroscopy in combination with partial least squares (PLS) regression is applied for the first time to the analysis of ethyl carbamate in stone fruit spirits () and unrecorded alcohols () (analysis time only 15 min per sample). The PLS procedure was validated using an independent set of samples (, ,  mg/L) in comparison to reference GC/MS/MS results. The NMR method was found to outperform other screening techniques based on NIR or FTIR regarding sensitivity and selectivity. The major advantage over GC/MS/MS, besides the reduced time of instrumental analysis, is that no sample preparation besides addition of buffer with internal standard is required, while for GC/MS/MS labour-intensive sample extraction is necessary prior to measurement.

Characterization of frozen hydrated biological specimens by low-loss EELS

1992 ◽  
Vol 50 (2) ◽  
pp. 1572-1573
Author(s):  
Songquan Sun ◽  
Richard D. Leapman
Keyword(s):  
Water Content ◽  
Direct Method ◽  
Internal Standard ◽  
Dry Weight ◽  
Dark Field ◽  
Protein Solutions ◽  
Subcellular Compartment ◽  
Differential Shrinkage ◽  
Electron Energy Loss

Analyses of ultrathin cryosections are generally performed after freeze-drying because the presence of water renders the specimens highly susceptible to radiation damage. The water content of a subcellular compartment is an important quantity that must be known, for example, to convert the dry weight concentrations of ions to the physiologically more relevant molar concentrations. Water content can be determined indirectly from dark-field mass measurements provided that there is no differential shrinkage between compartments and that there exists a suitable internal standard. The potential advantage of a more direct method for measuring water has led us to explore the use of electron energy loss spectroscopy (EELS) for characterizing biological specimens in their frozen hydrated state.We have obtained preliminary EELS measurements from pure amorphous ice and from cryosectioned frozen protein solutions. The specimens were cryotransfered into a VG-HB501 field-emission STEM equipped with a 666 Gatan parallel-detection spectrometer and analyzed at approximately −160 C.

SEM and TEM observations of sperm development in the testis of the freshwater fish Oreochromis mossambicus

1990 ◽  
Vol 48 (3) ◽  
pp. 58-59
Author(s):  
Daryl A. Cornish ◽  
George L. Smit
Keyword(s):  
Morphological Characteristics ◽  
Oreochromis Mossambicus ◽  
Breeding Cycle ◽  
Limited Information ◽  
North West ◽  
The North ◽  
Sem And Tem ◽  
Sperm Development ◽  
Ultrastructural Characteristics ◽  
The University

Oreochromis mossambicus is currently receiving much attention as a candidater species for aquaculture programs within Southern Africa. This has stimulated interest in its breeding cycle as well as the morphological characteristics of the gonads. Limited information is available on SEM and TEM observations of the male gonads. It is known that the testis of O. mossambicus is a paired, intra-abdominal structure of the lobular type, although further details of its characteristics are not known. Current investigations have shown that spermatids reach full maturity some two months after the female becomes gravid. Throughout the year, the testes contain spermatids at various stages of development although spermiogenesis appears to be maximal during November when spawning occurs. This paper describes the morphological and ultrastructural characteristics of the testes and spermatids.Specimens of this fish were collected at Syferkuil Dam, 8 km north- west of the University of the North over a twelve month period, sacrificed and the testes excised.

STEM measurement of subcellular water distributions

1993 ◽  
Vol 51 ◽  
pp. 568-569
Author(s):  
R.D. Leapman ◽  
S.Q. Sun ◽  
S-L. Shi ◽  
R.A. Buchanan ◽  
S.B. Andrews
Keyword(s):  
Water Content ◽  
Internal Standard ◽  
Dry Weight ◽  
Dry Mass ◽  
Scanning Transmission Electron Microscope ◽  
Dark Field ◽  
Bulk Water ◽  
Inelastic Electron ◽  
Scanning Transmission ◽  
Annular Dark Field

Recent advances in rapid-freezing and cryosectioning techniques coupled with use of the quantitative signals available in the scanning transmission electron microscope (STEM) can provide us with new methods for determining the water distributions of subcellular compartments. The water content is an important physiological quantity that reflects how fluid and electrolytes are regulated in the cell; it is also required to convert dry weight concentrations of ions obtained from x-ray microanalysis into the more relevant molar ionic concentrations. Here we compare the information about water concentrations from both elastic (annular dark-field) and inelastic (electron energy loss) scattering measurements.In order to utilize the elastic signal it is first necessary to increase contrast by removing the water from the cryosection. After dehydration the tissue can be digitally imaged under low-dose conditions, in the same way that STEM mass mapping of macromolecules is performed. The resulting pixel intensities are then converted into dry mass fractions by using an internal standard, e.g., the mean intensity of the whole image may be taken as representative of the bulk water content of the tissue.

Development of low-Gly m Bd 30K(P34) allergen breeding lines using molecular marker in soybean

Planta Medica ◽  
2011 ◽  
Vol 77 (12) ◽  
Author(s):  
J Kwang Ho ◽  
C Man Soo ◽  
L Suk Ki ◽  
S Min Jung ◽  
K Yul Ho ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Breeding Lines

On the Preparation of Bovine α-Thrombin

1978 ◽  
Vol 39 (01) ◽  
pp. 193-200 ◽  
Author(s):  
Erwin F Workman ◽  
Roger L Lundblad
Keyword(s):  
Immobilized Enzyme ◽  
Catalytic Properties ◽  
Specific Activity ◽  
Guanidine Hydrochloride ◽  
Low Molecular Weight ◽  
Reversible Process ◽  
Gel Beads ◽  
Tissue Thromboplastin ◽  
C 50 ◽  
Hydrolysis Of

SummaryAn improved method for the preparation of bovine α-thrombin is described. The procedure involves the activation of partially purified prothrombin with tissue thromboplastin followed by chromatography on Sulfopropyl-Sephadex C-50. The purified enzyme is homogeneous on polyacrylamide discontinuous gel electrophoresis and has a specific activity toward fibrinogen of 2,200–2,700 N.I.H. U/mg. Its stability on storage in liquid media is dependent on both ionic strenght and temperature. Increasing ionic strength and decreasing temperature result in optimal stability. The denaturation of α-thrombin by guanidine hydrochloride was found to be a partially reversible process with the renatured species possessing properties similar to “aged” thrombin. In addition, the catalytic properties of a-thrombin covalently attached to agarose gel beads were also examined. The activity of the immobilized enzyme toward fibrinogen was affected to a much greater extent than was the hydrolysis of low molecular weight, synthetic substrates.

Autómatas Celulares Aplicados al Comportamiento de Células de Cáncer Cervicouterino

2019 ◽  
Vol 6 (1) ◽  
pp. 44-49
Author(s):  
Tania Muñoz Jiménez ◽  
Aurora Torres Soto ◽  
María Dolores Torres Soto
Keyword(s):  
Cellular Automaton ◽  
Medical Model ◽  
Research Process ◽  
Simulation Algorithm ◽  
Stages Of Development ◽  
Literary Research ◽  
Migration Dynamics ◽  
Three Stages ◽  
And Migration ◽  
Best Parameters

En este documento se describe el desarrollo e implementación de un modelo para simular computacionalmente la dinámica del crecimiento y migración del cáncer cervicouterino, considerando sus principales características: proliferación, migración y necrosis, así como sus etapas de desarrollo. El modelo se desarrolló mediante un autómata celular con enfoques paralelo y secuencial. El autómata celular se basó en el modelo de Gompertz para simular las etapas de desarrollo de este cáncer, el cual se dividió en tres etapas cada una con diferentes comportamientos durante la simulación. Se realizó un diseño experimental con parámetros de entrada que se seleccionaron a partir de la investigación literaria y su discusión con médicos expertos. Al final del proceso de investigación, se logró obtener un algoritmo computacional de simulación muy bueno comparado con el modelo médico de Gompertz y se encontraron los mejores parámetros para su ejecución mediante un diseño factorial soportado estadísticamente. This paper describes the development and implementation of a model to computationally simulate the growth and migration dynamics of cervical cancer, considering its main characteristics: proliferation, migration and necrosis, as well as its stages of development. The model was developed by means of a cellular automaton with parallel and sequential approaches. The cellular automaton was based on the model of Gompertz to simulate the stages of development of this cancer, which was divided into three stages, each with different behaviors during the simulation. An experimental design was carried out with input parameters that were selected from literary research and its discussion with expert physicians. At the end of the research process, a very good simulation algorithm was obtained compared to the Gompertz medical model and the best parameters for its execution were found by means of a statistically supported factorial design.

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