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Comparative study on nutritional and technological properties of two varieties of black wheat flour and their noodle-making potential. J Food Sci 2024; 89:306-319. [PMID: 38018239 DOI: 10.1111/1750-3841.16857] [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: 02/01/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
Comparative studies were conducted on physicochemical and technological properties of two black wheat (BW) varieties (cultivated in Shanxi Agricultural University) and their noodle-making potential. Whole-grain BW noodles showed acceptable cooking loss (≤10%) and strong antioxidant capacity. However, their textural quality remains to be enhanced. Regarding refined flour (RF) of the two BW varieties, Yunhei 14207 showed more anthocyanins, brighter color, and greater thermal stability (as reflected by the higher pasting temperature). 16W16 resulted in greater gluten content and better gluten quality of flour and higher dough stability, which contributed to the lower cooking loss and stronger tensile property of noodles. RF noodles of Yunhei 14207 displayed brighter appearance, although they had weaker tensile property. The stronger gluten network in noodles of 16W16 protected phenolics from release and degradation during drying, cooking, and steaming. Despite phenolics loss, RF noodles of Yunhei 14207 showed antioxidant capacity up to 14.97 mg TE/100 g. This research would promote understanding of characteristics of BW varieties. Considering the stronger gluten network of 16W16, its fortification in common wheat noodles at high proportion (>50%) may be promising to develop antioxidant noodles with further improved sensory quality.
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Effect of temperature and protein concentration on the protein types within the ultracentrifugation supernatant of liquid micellar casein concentrate. J Dairy Sci 2023; 106:8331-8340. [PMID: 37641294 DOI: 10.3168/jds.2023-23595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/05/2023] [Indexed: 08/31/2023]
Abstract
Liquid micellar casein concentrate (MCC) is an ideal milk-based protein ingredient for neutral-pH ready-to-drink beverages. The texture and mouthfeel of liquid MCC-based beverages depend on the beverage protein content, as well as the composition of soluble proteins in the aqueous phase around the casein micelle. The objective of this study was to determine the composition of soluble proteins in the aqueous phase around the casein micelles in skim milk and liquid MCC containing 7.0% and 11.6% protein content. Skim milk was pasteurized and concentrated to 7% protein content by microfiltration and then to 18% protein content by ultrafiltration. The 18% MCC was then serially diluted with distilled water to produce 11.6% and 7.0% protein MCC. Skim milk, 7.0% MCC, and 11.6% MCC representing starting materials with different protein concentrations were each ultracentrifuged at 100,605 × g for 2 h. The ultracentrifugation for each of the starting materials was performed at 3 different temperatures: 4°C, 20°C, and 37°C. The ultracentrifugation supernatants were collected to represent the aqueous phase around the casein micelle in MCC solutions. The supernatants were analyzed by Kjeldahl to determine the crude protein, casein, and casein as a percentage of crude protein content, and by sodium dodecyl sulfate PAGE to determine the composition of the individual proteins. Most of the proteins in MCC supernatant (about 45%) were casein proteolysis products. The remaining proteins in the MCC supernatant consisted of a combination of intact αS-, β-, and κ-caseins (about 40%) and serum proteins (14-18%). Concentrations of αS-casein and β-casein in the supernatant increased with decreasing temperature, especially at higher protein concentrations. Temperature and interaction between temperature and protein explained about 80% of the variation in concentration of supernatant αS- and β-caseins. Concentration of supernatant κ-casein, casein proteolysis products, and serum protein increased with increasing MCC protein concentration, and MCC protein concentration explained most of the variation in supernatant κ-casein, casein proteolysis products, and serum protein concentrations. Predicted MCC apparent viscosity was positively associated with the dissociation of αS- and β-caseins. Optimal beverage viscosity could be achieved by controlling the dissociation of these proteins in MCC.
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Effects of Starch Molecular Structure and Physicochemical Properties on Eating Quality of Indica Rice with Similar Apparent Amylose and Protein Contents. Foods 2023; 12:3535. [PMID: 37835188 PMCID: PMC10572605 DOI: 10.3390/foods12193535] [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: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
It is important to clarify the effects of starch fine structure and protein components on the eating quality of indica rice. In this study, seven indica rice varieties with similar apparent amylose content (AAC) and protein content (PC) but different sensory taste values were selected and compared systematically. It was found that except for AAC and PC, these varieties showed significant differences in starch molecular structure and protein components. Compared with rice varieties with a low sensory taste value, varieties with a higher sensory taste value showed significantly lower amylose and higher amylopectin short chains (degree of polymerization 6-12) content; the protein component showed that the varieties with good taste value had higher albumin and lower globulin and glutelin content (p < 0.05). Rice varieties with lower AC, globulin, and glutelin content, as well as a higher content of albumin and amylopectin short chains, resulted in a higher swelling factor, peak viscosity, breakdown value, and ratio of hardness to stickiness, in which condition cooked rice showed a higher sensory taste value. Moreover, this study indicated that rice varieties with a higher content of albumin and amylopectin short chains were conducive to the good appearance of cooked rice. This study lays the foundation for the taste evaluation of good-tasting indica rice.
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Clipping Effect on the Grain Nitrogen and Protein Fractions of Ancient and Old Wheats Grown in a Mediterranean Environment. Foods 2023; 12:2582. [PMID: 37444319 DOI: 10.3390/foods12132582] [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: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
This study is the first to assess the effects of clipping, cultivar, season, and their interactions on the protein composition of six old and ancient wheat cultivars (n = 6). For this, nitrogen content, the proportion of wheat protein fractions, and the molecular weight distribution of the extractable and unextractable glutenin polymers were investigated as a function of cultivar and clipping in two consecutive seasons. The relationships between genotypic variation in grain nitrogen and protein fraction content under clipping and non-clipping conditions were also assessed. Clipping delayed and shortened the grain filling period of all of the cultivars. The protein composition of some cultivars behaved differently to clipping due to differences in the environmental conditions of S1 (exceptional dry season) and S2 (rainy season). In S1, clipping decreased the ratio of gliadins over glutenins (GLI/GLU) (<1) of Cappelli and Giovanni Paolo, while in S2, clipping improved the GLI/GLU of Giovanni Paolo, Monlis, and Norberto. The unextractable polymeric proteins were not affected by clipping. Khorasan was shown to be indifferent to clipping in S1 and S2. These results suggest that it is possible to have ancient/old wheats suitable for a dual-purpose system, in different climatic conditions, while maintaining good grain quality traits. The increased market demand for ancient and old wheats presents an economic opportunity for farmers who adopt the dual-purpose technique to cultivate these resilient crops again and increase their profit margins and revenues.
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pH-dependent sedimentation and protein interactions in ultra-high-temperature-treated sheep skim milk. J Dairy Sci 2023; 106:1626-1637. [PMID: 36543644 DOI: 10.3168/jds.2022-22637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/27/2022] [Indexed: 12/23/2022]
Abstract
Sheep milk is considered unstable to UHT processing, but the instability mechanism has not been investigated. This study assessed the effect of UHT treatment (140°C/5 s) and milk pH values from 6.6 to 7.0 on the physical properties of sheep skim milk (SSM), including heat coagulation time, particle size, sedimentation, ionic calcium level, and changes in protein composition. Significant amounts of sediment were found in UHT-treated SSM at the natural pH (∼6.6) and pH 7.0, whereas lower amounts of sediment were observed at pH values of 6.7 to 6.9. The proteins in the sediment were mainly κ-casein (CN)-depleted casein micelles with low levels of whey proteins regardless of the pH. Both the pH and the ionic calcium level of the SSM at all pH values decreased after UHT treatment. The dissociation levels of κ-, β-, and αS2-CN increased with increasing pH of the SSM before and after heating. The protein content, ionic calcium level, and dissociation level of κ-CN were higher in the SSM than values reported previously in cow skim milk. These differences may contribute to the high amounts of sediment in the UHT-treated SSM at natural pH (∼6.6). Significantly higher levels of κ-, β-, and αS2-CN were detected in the serum phase after heating the SSM at pH 7.0, suggesting that less κ-CN was attached to the casein micelles and that more internal structures of the casein micelles may have been exposed during heating. This could, in turn, have destabilized the casein micelles, resulting in the formation of protein aggregates and high amounts of sediment after UHT treatment of the SSM at pH 7.0.
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Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models. J Comput Biol 2023; 30:204-222. [PMID: 36251780 DOI: 10.1089/cmb.2022.0241] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In the last three decades, a wide range of protein features have been discovered to annotate a protein. Numerous attempts have been made to integrate these features in a software package/platform so that the user may compute a wide range of features from a single source. To complement the existing methods, we developed a method, Pfeature, for computing a wide range of protein features. Pfeature allows to compute more than 200,000 features required for predicting the overall function of a protein, residue-level annotation of a protein, and function of chemically modified peptides. It has six major modules, namely, composition, binary profiles, evolutionary information, structural features, patterns, and model building. Composition module facilitates to compute most of the existing compositional features, plus novel features. The binary profile of amino acid sequences allows to compute the fraction of each type of residue as well as its position. The evolutionary information module allows to compute evolutionary information of a protein in the form of a position-specific scoring matrix profile generated using Position-Specific Iterative Basic Local Alignment Search Tool (PSI-BLAST); fit for annotation of a protein and its residues. A structural module was developed for computing of structural features/descriptors from a tertiary structure of a protein. These features are suitable to predict the therapeutic potential of a protein containing non-natural or chemically modified residues. The model-building module allows to implement various machine learning techniques for developing classification and regression models as well as feature selection. Pfeature also allows the generation of overlapping patterns and features from a protein. A user-friendly Pfeature is available as a web server python library and stand-alone package.
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Gradients of Orientation, Composition, and Hydration of Proteins for Efficient Light Collection by the Cornea of the Horseshoe Crab. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203371. [PMID: 36251923 PMCID: PMC9685478 DOI: 10.1002/advs.202203371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/30/2022] [Indexed: 06/16/2023]
Abstract
The lateral eyes of the horseshoe crab, Limulus polyphemus, are the largest compound eyes within recent Arthropoda. The cornea of these eyes contains hundreds of inward projecting elongated cuticular cones and concentrate light onto proximal photoreceptor cells. Although this visual system has been extensively studied before, the precise mechanism allowing vision has remained controversial. Correlating high-resolution quantitative refractive index (RI) mapping and structural analysis, it is demonstrated how gradients of RI in the cornea stem from structural and compositional gradients in the cornea. In particular, these RI variations result from the chitin-protein fibers architecture, heterogeneity in protein composition, and bromine doping, as well as spatial variation in water content resulting from matrix cross-linking on the one hand and cuticle porosity on the other hand. Combining the realistic cornea structure and measured RI gradients with full-wave optical modeling and ray tracing, it is revealed that the light collection mechanism switches from refraction-based graded index (GRIN) optics at normal light incidence to combined GRIN and total internal reflection mechanism at high incident angles. The optical properties of the cornea are governed by different mechanisms at different hierarchical levels, demonstrating the remarkable versatility of arthropod cuticle.
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Anisotropic Composition and Mechanical Behavior of a Natural Thin-Walled Composite: Eagle Feather Shaft. Polymers (Basel) 2022; 14:polym14020309. [PMID: 35054715 PMCID: PMC8780336 DOI: 10.3390/polym14020309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Flight feather shafts are outstanding bioinspiration templates due to their unique light weight and their stiff and strong characteristics. As a thin wall of a natural composite beam, the keratinous cortex has evolved anisotropic features to support flight. Here, the anisotropic keratin composition, tensile response, dynamic properties of the cortex, and fracture behaviors of the shafts are clarified. The analysis of Fourier transform infrared (FTIR) spectra indicates that the protein composition of calamus cortex is almost homogeneous. In the middle and distal shafts (rachis), the content of the hydrogen bonds (HBs) and side-chain is the highest within the dorsal cortex and is consistently lower within the lateral wall. The tensile responses, including the properties and dominant damage pattern, are correlated with keratin composition and fiber orientation in the cortex. As for dynamic properties, the storage modulus and damping of the cortex are also anisotropic, corresponding to variation in protein composition and fibrous structure. The fracture behaviors of bent shafts include matrix breakage, fiber dissociation and fiber rupture on compressive dorsal cortex. To clarify, ‘real-time’ damage behaviors, and an integrated analysis between AE signals and fracture morphologies, are performed, indicating that calamus failure results from a straight buckling crack and final fiber rupture. Moreover, in the dorsal and lateral walls of rachis, the matrix breakage initially occurs, and then the propagation of the crack is restrained by ‘ligament-like’ fiber bundles and cross fiber, respectively. Subsequently, the further matrix breakage, interface dissociation and induced fiber rupture in the dorsal cortex result in the final failure.
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Influences of grain and protein characteristics on in vitro protein digestibility of modern and ancient wheat species. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:4578-4584. [PMID: 33474737 DOI: 10.1002/jsfa.11100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/12/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The resistance of proteins to gastrointestinal digestion contributes to their ability to act as allergens. Near-complete digestion of protein in wheat products is important with respect to avoiding the potential immunogenic effects of undigested peptides. Five modern US wheat classes (soft red winter, hard winter, hard red spring, club and durum) including 17 wheat varieties, as well as three ancient wheat classes (spelt, emmer and einkorn) including nine wheat varieties, were analyzed for kernel hardness (KH) and flour protein characteristics, in addition to in vitro protein digestibility (IVPD) of cooked flour, flour without albumins and globulins (FWOAG), gluten, albumins, and globulins, aiming to identify the factors influencing the protein digestibility of flour. RESULTS IVPDs of flour, FWOAG, gluten and albumins of wheat varieties ranged from 86.5% to 92.3%, 85.8% to 90.3%, 90.6% to 94.6% and 74.8% to 85.1%, respectively. The IVPD of gluten was significantly higher than the IVPDs of flour and FWOAG, indicating that non-protein components substantially affect protein digestibility. Significant differences were observed in IVPDs of flour and albumins among eight wheat classes, but not in the IVPDs of FWOAG, gluten and globulins. There were apparent differences in undigested protein bands and intensities of wheat classes with low and high flour IVPDs. KH and albumin proportion exhibited negative and positive relationships, respectively, with flour IVPD. CONCLUSION The results of the present study demonstrate that KH, non-protein components and albumin proportion have a major influence on protein digestion and need to be considered when developing wheat cultivars with higher protein digestibility.
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Abstract
Biomaterials, once inserted in the oral cavity, become immediately covered by a layer of adsorbed proteins that consists mostly of salivary proteins but also of plasma proteins if the biomaterial is placed close to the gingival margin or if it becomes implanted into tissue and bone. It is often this protein layer, rather than the pristine biomaterial surface, that is subsequently encountered by colonizing bacteria or attaching tissue cells. Thus, to study this important initial protein adsorption from human saliva and serum and how it might be influenced through chemical modification of the biomaterial surface, we have measured the amount of protein adsorbed and analyzed the composition of the adsorbed protein layer using gel electrophoresis and western blotting. Here, we have developed an in vitro model system based on silica surfaces, chemically modified with 7 silane-based self-assembled monolayers that span a broad range of physicochemical properties, from hydrophilic to hydrophobic surfaces (water contact angles from 15° to 115°), low to high surface free energy (12 to 57 mN/m), and negative to positive surface charge (zeta potentials from –120 to +40 mV at physiologic pH). We found that the chemical surface functionalities exerted a substantial effect on the total amounts of proteins adsorbed; however, no linear correlation of the adsorbed amounts with the physicochemical surface parameters was observed. Only the adsorption behavior of a few singular protein components, from which physicochemical data are available, seems to follow physicochemical expectations. Examples are albumin in serum and lysozyme in saliva; in both, adsorption was favored on countercharged surfaces. We conclude from these findings that in complex biofluids such as saliva and serum, adsorption behavior is dominated by the overall protein-binding capacity of the surface rather than by specific physicochemical interactions of single protein entities with the surface.
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Proteomic analysis of oilseed cake: a comparative study of species-specific proteins and peptides extracted from ten seed species. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:297-306. [PMID: 32629549 DOI: 10.1002/jsfa.10643] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/06/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND In recent years there has been a visible trend among consumers to move away from consuming meat in favor of plant products. Meat producers have therefore been trying to meet the expectations of consumers by introducing new products to the food market with a greater proportion of plant ingredients. Meat products are enriched not only by the addition of vegetable oils but also by ground or whole oilseeds or their preparation. In this study, we present in-solution tryptic digestion and an ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS)-based proteomics approach to investigate specific proteins and peptides of ten oilseed cakes, by-products of cold pressing oil from coconut, evening primrose, hemp, flax, milk thistle, nigella, pumpkin, rapeseed, sesame, and sunflower seeds, for authentication purposes. RESULTS We identified a total of 229 unique oilseed proteins. The number of specific proteins varied depending on the sample, from 4 to 48 in evening primrose and sesame. Moreover, we identified approximately 440 oilseed unique peptides in the cakes of all the analyzed oilseeds; the largest amounts were found in sesame (107 peptides), sunflower (100), pumpkin, hemp (42), rapeseed (36), and flax cake (35 peptides). CONCLUSIONS We provide novel information on unique / species-specific peptide markers that will extend the scope of testing the authenticity of a wide range of foods. The results of this peptide discovery experiment may further contribute to the development of targeted methods for the detection and quantification of oilseed proteins in processed foods, and thus to the improvement of food quality. © 2020 Society of Chemical Industry.
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The Nutritional Value and Biological Activity of Concentrated Protein Fraction of Potato Juice. Nutrients 2019; 11:E1523. [PMID: 31277482 PMCID: PMC6683274 DOI: 10.3390/nu11071523] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 01/27/2023] Open
Abstract
Potato protein is recognized as one of the most valuable nonanimal proteins due to the high content of essential amino acids. So far, it has not been used in human nutrition on a large scale due to technological limitations regarding its acquisition. In this study, the protein fraction of potato juice was concentrated with the use of membrane separation. The obtained potato juice protein concentrate (PJPC) was characterized in terms of nutritional value and biological activity, and the amino acid composition, mineral content, and antioxidant properties were determined. Moreover, in vitro cytotoxic activity against cancer cells of the gastrointestinal tract was investigated. The results of the present study indicate that PJPC is an excellent source of lysine and threonine, while leucine is its limiting amino acid, with an amino acid score (AAS) of 65%. Moreover, PJPC contains substantial amounts of Fe, Mn, K, and Cu. As demonstrated experimentally, PJPC is also characterized by higher antioxidant potential than potato itself. Biological activity, however, is not limited to antioxidant activity alone. Cytotoxicity studies using a gastric cancer cell line (Hs 746T), a colon cancer cell line (HT-29), and human colon normal cells (CCD 841 CoN) proved that PJPC is characterized by selective activity against cancer cells. It can thus be concluded that the developed method of producing protein concentrate from potato juice affords a product with moderate nutritional value and interesting biological activity.
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Effect of Sterilization Process and Storage on the Antioxidative Properties of Runner Bean. Molecules 2018; 23:E1409. [PMID: 29891759 PMCID: PMC6100000 DOI: 10.3390/molecules23061409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 05/07/2018] [Accepted: 06/05/2018] [Indexed: 12/27/2022] Open
Abstract
In this study, we investigated the effect of standard preservation of bean seeds on changes in contents and activity of their selected components: dry matter, ash, different forms of nitrogen, composition of protein fractions; total phenolics and condensed tannins; ability to chelate iron(II) ions; antiradical activity against ABTS•+ and DPPH•; and capability for inhibiting autoxidation and enzymatic oxidation of linoleic acid. The conducted technological process caused various changes in contents of nitrogen forms and partial loss of phenolic compounds. The antiradical and antioxidative activity of the extracts decreased significantly, while an increase was observed in their ability to chelate Fe(II). These changes were due to the migration of active compounds to the brine, and to their structural transformations and degradation. Longer storage of the sterilized product caused restoration of part of the antiradical activity of the seeds.
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Proteome Evolution of Deep-Sea Hydrothermal Vent Alvinellid Polychaetes Supports the Ancestry of Thermophily and Subsequent Adaptation to Cold in Some Lineages. Genome Biol Evol 2017; 9:279-296. [PMID: 28082607 PMCID: PMC5381640 DOI: 10.1093/gbe/evw298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 12/22/2022] Open
Abstract
Temperature, perhaps more than any other environmental factor, is likely to influence the evolution of all organisms. It is also a very interesting factor to understand how genomes are shaped by selection over evolutionary timescales, as it potentially affects the whole genome. Among thermophilic prokaryotes, temperature affects both codon usage and protein composition to increase the stability of the transcriptional/translational machinery, and the resulting proteins need to be functional at high temperatures. Among eukaryotes less is known about genome evolution, and the tube-dwelling worms of the family Alvinellidae represent an excellent opportunity to test hypotheses about the emergence of thermophily in ectothermic metazoans. The Alvinellidae are a group of worms that experience varying thermal regimes, presumably having evolved into these niches over evolutionary times. Here we analyzed 423 putative orthologous loci derived from 6 alvinellid species including the thermophilic Alvinella pompejana and Paralvinella sulfincola. This comparative approach allowed us to assess amino acid composition, codon usage, divergence, direction of residue changes and the strength of selection along the alvinellid phylogeny, and to design a new eukaryotic thermophilic criterion based on significant differences in the residue composition of proteins. Contrary to expectations, the alvinellid ancestor of all present-day species seems to have been thermophilic, a trait subsequently maintained by purifying selection in lineages that still inhabit higher temperature environments. In contrast, lineages currently living in colder habitats likely evolved under selective relaxation, with some degree of positive selection for low-temperature adaptation at the protein level.
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Cow and environmental factors associated with protein fractions and free amino acids predicted using mid-infrared spectroscopy in bovine milk. J Dairy Sci 2017. [PMID: 28624276 DOI: 10.3168/jds.2016-12410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The objective of the present study was to identify the factors associated with both the protein composition and free amino acid (FAA) composition of bovine milk predicted using mid-infrared spectroscopy. Milk samples were available from 7 research herds and 69 commercial herds. The spectral data from the research herds comprised 94,286 separate morning and evening milk samples; the spectral data from the commercial herds comprised 40,260 milk samples representing a composite sample of both the morning and evening milkings. Mid-infrared spectroscopy prediction models developed in a previous study were applied to all spectra. Factors associated with the predicted protein and FAA composition were quantified using linear mixed models. Factors considered in the model included the fixed effects of calendar month of the test, milking time (i.e., morning, evening, or both combined), parity (1, 2, 3, 4, 5, and ≥6), stage of lactation, the interaction between parity and stage of lactation, breed proportion of the cow (Friesian, Jersey, Norwegian Red, Montbéliarde, and other), and both the general heterosis and recombination coefficients of the cow. Contemporary group as well as both within- and across-lactation permanent environmental effects were included in all models as random effects. Total proteins (i.e., total casein, CN; total whey; and total β-lactoglobulin) and protein fractions (with the exception of α-lactalbumin) decreased postcalving until 36 to 65 days in milk and increased thereafter. After adjusting the statistical model for differences in crude protein content and milk yield separately, irrespective of stage of lactation, younger animals produced more total proteins (i.e., total CN, total whey, and total β-lactoglobulin) as well as more total FAA, Glu, and Asp than their older contemporaries. The concentration of all protein fractions (except β-CN) in milk was greatest in the evening milk, even after adjusting for differences in the crude protein content of the milk. Relative to a purebred Holstein cow, Jersey cows, on average, produced a greater concentration of all CN fractions but less total FAA, Glu, Gly, Asp, and Val in milk. Relative to their respective purebred parental average, first-cross cows produced more total CN and more β-CN. Results from the present study indicate that many cow-level factors, as well as other factors, are associated with protein composition and FAA composition of bovine milk.
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Short communication: Mid-infrared spectroscopy prediction of fine milk composition and technological properties in Italian Simmental. J Dairy Sci 2016; 99:8216-8221. [PMID: 27497897 DOI: 10.3168/jds.2016-10953] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/21/2016] [Indexed: 11/19/2022]
Abstract
The objective of this study was to evaluate the ability of mid-infrared predictions of fine milk composition and technological traits to serve as a tool for large-scale phenotyping of the Italian Simmental population. Calibration equations accurately predicted the fatty acid profile of the milk, but we obtained moderate or poor accuracy for detailed protein composition, coagulation properties, curd yield and composition, lactoferrin, and concentration of major minerals. To evaluate the role of infrared predictions as indicator traits of fine milk composition in indirect selective breeding programs, the genetic parameters of the traits predicted using mid-infrared spectra need to be estimated.
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Abstract
Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.
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Release behavior of non-network proteins and its relationship to the structure of heat-induced soy protein gels. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4211-4219. [PMID: 25842998 DOI: 10.1021/acs.jafc.5b00132] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Heat-induced soy protein gels were prepared by heating protein solutions at 12%, 15% ,or 18% for 0.5, 1.0, or 2.0 h. The release of non-network proteins from gel slices was conducted in 10 mM pH 7.0 sodium phosphate buffer. SDS-PAGE and diagonal electrophoresis demonstrated that the released proteins consisted of undenatured AB subunits and denatured proteins including monomers of A polypeptides, disulfide bond linked dimers, trimers, and polymers of A polypeptides, and an unidentified 15 kDa protein. SEC-HPLC analysis of non-network proteins revealed three major protein peaks, with molecular weights of approximately 253.9, 44.8, and 9.7 kDa. The experimental data showed that the time-dependent release of the three fractions from soy protein gels fit Fick's second law. An increasing protein concentration or heating time resulted in a decrease in diffusion coefficients of non-network proteins. A power law expression was used to describe the relationship between non-network protein diffusion coefficient and molecular weight, for which the exponent (α) shifted to higher value with an increase in protein concentration or heating time, indicating that a more compact gel structure was formed.
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Effects of soybean protein composition and processing conditions on silken tofu properties. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:3065-71. [PMID: 23512756 DOI: 10.1002/jsfa.6140] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 02/06/2013] [Accepted: 03/19/2013] [Indexed: 06/01/2023]
Abstract
BACKGROUND Texture and water holding are important for silken tofu manufacturers and are affected by many factors, including soybean variety and processing conditions. In this study we evaluated these two key quality attributes of silken tofu produced from two soybean varieties - Bunya and Cowrie - using a soak or a dry processing method with glucono-δ-lactone or nigari as coagulant at concentrations of 1.5-5.0 g kg⁻¹. RESULTS The soak method produced substantially firmer silken tofu with either coagulant. The optimum coagulant concentration to achieve maximum hardness was 2.5-3.0 g kg⁻¹. At 3.0 g kg⁻¹, Bunya produced silken tofu with firmer texture for each of the coagulant-method combinations and lower water loss, an indicator for water holding capacity, for the soak method. The two varieties differed significantly in the composition of major protein subunits for the seed and soymilk. Bunya had no 11SA4, less 11S and more 7S and therefore a lower 11S/7S ratio. CONCLUSION Both variety and processing conditions affect textural properties and water loss of silken tofu. The absence of 11SA4 and subsequent protein subunit compositions are important in determining these two key quality attributes. Variety Bunya produces silken tofu with firmer texture and lower water loss.
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The occurrence of noncoagulating milk and the association of bovine milk coagulation properties with genetic variants of the caseins in 3 Scandinavian dairy breeds. J Dairy Sci 2013; 96:4830-42. [PMID: 23746587 DOI: 10.3168/jds.2012-6422] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/22/2013] [Indexed: 11/19/2022]
Abstract
Substantial variation in milk coagulation properties has been observed among dairy cows. Consequently, raw milk from individual cows and breeds exhibits distinct coagulation capacities that potentially affect the technological properties and milk processing into cheese. This variation is largely influenced by protein composition, which is in turn affected by underlying genetic polymorphisms in the major milk proteins. In this study, we conducted a large screening on 3 major Scandinavian breeds to resolve the variation in milk coagulation traits and the frequency of milk with impaired coagulation properties (noncoagulation). In total, individual coagulation properties were measured on morning milk collected from 1,299 Danish Holstein (DH), Danish Jersey (DJ), and Swedish Red (SR) cows. The 3 breeds demonstrated notable interbreed differences in coagulation properties, with DJ cows exhibiting superior coagulation compared with the other 2 breeds. In addition, milk samples from 2% of DH and 16% of SR cows were classified as noncoagulating. Furthermore, the cows were genotyped for major genetic variants in the αS1- (CSN1S1), β- (CSN2), and κ-casein (CSN3) genes, revealing distinct differences in variant frequencies among breeds. Allele I of CSN2, which had not formerly been screened in such a high number of cows in these Scandinavian breeds, showed a frequency around 7% in DH and DJ, but was not detected in SR. Genetic polymorphisms were significantly associated with curd firming rate and rennet coagulation time. Thus, CSN1S1 C, CSN2 B, and CSN3 B positively affected milk coagulation, whereas CSN2 A(2), in particular, had a negative effect. In addition to the influence of individual casein genes, the effects of CSN1S1-CSN2-CSN3 composite genotypes were also examined, and revealed strong associations in all breeds, which more or less reflected the single gene results. Overall, milk coagulation is under the influence of additive genetic variation. Optimal milk for future cheese production can be ensured by monitoring the frequency of unfavorable variants and thus preventing an increase in the number of cows producing milk with impaired coagulation. Selective breeding for variants associated with superior milk coagulation can potentially increase raw milk quality and cheese yield in all 3 Scandinavian breeds.
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COMPARATIVE STUDIES ON THE SUB-UNIT COMPOSITION OF THE ALBUMINS, VICILINS AND LEGUMINS OF ISOLATED PROTEIN BODIES FROM COTYLEDONS OF DRY SEEDS OF TWO MEMBERS OF THE LEGUMINOSAE: CYTISUS SCOPARIUS (L.) LINK AND C. SCOPARIUS SSP. MARITIMUS (ROUY) HEYWOOD. THE NEW PHYTOLOGIST 1986; 102:65-72. [PMID: 33873892 DOI: 10.1111/j.1469-8137.1986.tb00798.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The isolated protein bodies of Cytisus scoparius (L.) Link and Cytisus scoparius ssp. maritimus (Rouy) Heywood were observed by scanning electron microscopy; they showed comparable shapes and sizes. The protein content and the sub-unit composition of the fractionated albumins, vicilins and legumins, however, showed significant electrophoretic differences between the two plants, both at the qualitative and quantitative levels.
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The cortex of Xenopus laevis embryos: regional differences in composition and biological activity. Proc Natl Acad Sci U S A 1971; 68:2921-3. [PMID: 5289235 PMCID: PMC389560 DOI: 10.1073/pnas.68.12.2921] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The cortex of fertilized Xenopus laevis eggs undergoes regional changes in its composition and morphogenetic activity during the first three divisions. Gray crescent and animal pole cortex of stage 1 (1-cell) and stage 4 (8-cell) embryos each contain a characteristic array of proteins. Implantation of pieces of cortex into the blastocoel of midblastula embryos was used to assay their inductive capacity. The gray crescent cortex was shown to be the only region that had significant axis-inducing activity. This activity increased from stage 1 to stage 4.
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