A chemometric approach to evaluate the impact of pulses,
            Chlorella
            and
            Spirulina
            on proximate composition, amino acid, and physicochemical properties of turkey burgers

The objective of the current work was to demonstrate the equivalence of Mylan’s glatiramer acetate (GA) to that of the reference product Copaxone® (COP) using the four criteria for active pharmaceutical ingredient sameness as established by the US Food and Drug Administration (FDA). The reaction scheme used to produce Mylan’s glatiramer acetate (MGA) was compared with that of COP, determined from publicly available literature. Comparative analyses of MGA and COP were performed for physicochemical properties such as amino acid composition and molecular weight distributions. Spectroscopic fingerprints were obtained using circular dichroism spectroscopy. Structural signatures for polymerization and depolymerization including total diethylamine (DEA) content, relative proportions of DEA-adducted amino acids, and N-and C-terminal amino acid sequences were probed with an array of highly sensitive analytical methods. Biological activity of the products was assessed using validated murine Experimental autoimmune encephalomyelitis (EAE) models of multiple sclerosis. MGA is produced using the same fundamental reaction scheme as COP and was shown to have equivalent physicochemical properties and composition. Analyses of multiple structural signatures demonstrated equivalence of MGA and COP with regard to polymerization, depolymerization, and propagational shift. Examination of the impact on prevention and treatment of EAE demonstrated equivalence of MGA and COP with respect to both activity and toxicity, and thereby provided confirmatory evidence of sameness. A rigorous, multi-pronged comparison of MGA and COP produced using an equivalent fundamental reaction scheme demonstrated equivalent physicochemical properties, structural signatures for polymerization and depolymerization, and biological activity as evidenced by comparable effects in EAE. These studies demonstrate the equivalence of MGA and COP, establishing active ingredient sameness by the US Food and Drug Administration (FDA) criteria for GA, and provide compelling evidence that the FDA-approved generic MGA can be substituted for COP for the treatment of patients with relapsing-remitting MS.

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Teff Grain Physical and Chemical Quality Responses to Soil Physicochemical Properties and the Environment

Agronomy ◽

10.3390/agronomy9060283 ◽

2019 ◽

Vol 9 (6) ◽

pp. 283 ◽

Cited By ~ 4

Author(s):

Anteneh Abewa ◽

Enyew Adgo ◽

Birru Yitaferu ◽

Getachew Alemayehu ◽

Kebebew Assefa ◽

...

Keyword(s):

Amino Acid ◽

Physicochemical Properties ◽

Amino Acid Composition ◽

Acid Composition ◽

Proximate Composition ◽

Soil Samples ◽

Mineral Concentration ◽

Grain Color ◽

Management Interventions

Teff is the only cultivated cereal crop from the genus Eragrostis and it is the major staple food of Ethiopians. In Ethiopia, the quality of teff and its market price are primarily determined by its grain color. The objective of this study was to evaluate the effects of soil physicochemical characteristics across multiple locations in the two main teff growing regions of Amhara and Oromia states in Ethiopia on teff grain color and nutritional quality of a single variety. Grain and soil samples were collected from 24 field sites cultivated with the popular teff variety ‘Quncho’ (DZ-Cr-387/RIL-355). The teff grain samples collected from the 24 locations were evaluated for grain color, proximate composition, amino acid composition, and grain mineral concentration and the soil samples were analyzed for their physicochemical properties. Sample location means were considered different p < 0.05. Teff grain color indices of hue (H), saturation (S), and brightness (V), grain proximate composition, amino acid composition, and mineral concentration differed among locations (p < 0.05). There were significant negative correlations between grain S color value and soil pH, SOC, Ca, Mg, S, and Na. Soils with greater pH, SOC, Ca, Mg, and S generally had lower S values and thus, whiter color teff grains. There were considerable variations in the measured parameters for soil and teff grain physicochemical properties. The results indicated an opportunity for management interventions necessary to obtain uniformity in grain color and chemical composition for the same variety of teff grown in the two major regions in Ethiopia.

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Faculty Opinions recommendation of The use of orthologous sequences to predict the impact of amino acid substitutions on protein function.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.3558956.3485081 ◽

2010 ◽

Author(s):

Alejandro Schaffer

Keyword(s):

Amino Acid ◽

Protein Function ◽

Amino Acid Substitutions ◽

The Impact

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Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach

Recent Patents on Biotechnology ◽

10.2174/1872208314666200324114441 ◽

2020 ◽

Vol 14 (3) ◽

pp. 235-246

Author(s):

Sara Abdollahi ◽

Mohammad H. Morowvat ◽

Amir Savardashtaki ◽

Cambyz Irajie ◽

Sohrab Najafipour ◽

...

Keyword(s):

Amino Acid ◽

Physicochemical Properties ◽

Sequence Alignment ◽

Multiple Sequence Alignment ◽

In Silico ◽

Bacterial Species ◽

Arginine Deiminase ◽

Antitumor Effects ◽

Multiple Sequence ◽

In Silico Studies

Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.

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Combinations of Freeze-Dried Amorphous Vardenafil Hydrochloride with Saccharides as A Way to Enhance Dissolution Rate and Permeability

Pharmaceuticals ◽

10.3390/ph14050453 ◽

2021 ◽

Vol 14 (5) ◽

pp. 453

Author(s):

Gabriela Wiergowska ◽

Dominika Ludowicz ◽

Kamil Wdowiak ◽

Andrzej Miklaszewski ◽

Kornelia Lewandowska ◽

...

Keyword(s):

Physicochemical Properties ◽

Density Functional ◽

Hydroxypropyl Methylcellulose ◽

Fold Increase ◽

Crystalline Form ◽

Amorphous Form ◽

Freeze Dried ◽

Apparent Solubility ◽

Gastrointestinal Epithelium ◽

The Impact

To improve physicochemical properties of vardenafil hydrochloride (VAR), its amorphous form and combinations with excipients—hydroxypropyl methylcellulose (HPMC) and β-cyclodextrin (β-CD)—were prepared. The impact of the modification on physicochemical properties was estimated by comparing amorphous mixtures of VAR to their crystalline form. The amorphous form of VAR was obtained as a result of the freeze-drying process. Confirmation of the identity of the amorphous dispersion of VAR was obtained through the use of comprehensive analysis techniques—X-ray powder diffraction (PXRD) and differential scanning calorimetry (DSC), supported by FT-IR (Fourier-transform infrared spectroscopy) coupled with density functional theory (DFT) calculations. The amorphous mixtures of VAR increased its apparent solubility compared to the crystalline form. Moreover, a nearly 1.3-fold increase of amorphous VAR permeability through membranes simulating gastrointestinal epithelium as a consequence of the changes of apparent solubility (Papp crystalline VAR = 6.83 × 10−6 cm/s vs. Papp amorphous VAR = 8.75 × 10−6 cm/s) was observed, especially for its combinations with β-CD in the ratio of 1:5—more than 1.5-fold increase (Papp amorphous VAR = 8.75 × 10−6 cm/s vs. Papp amorphous VAR:β-CD 1:5 = 13.43 × 10−6 cm/s). The stability of the amorphous VAR was confirmed for 7 months. The HPMC and β-CD are effective modifiers of its apparent solubility and permeation through membranes simulating gastrointestinal epithelium, suggesting a possibility of a stronger pharmacological effect.

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HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires

Vaccines ◽

10.3390/vaccines9030270 ◽

2021 ◽

Vol 9 (3) ◽

pp. 270

Author(s):

Nicky de Vrij ◽

Pieter Meysman ◽

Sofie Gielis ◽

Wim Adriaensen ◽

Kris Laukens ◽

...

Keyword(s):

Amino Acid ◽

Cell Epitope ◽

Human Leukocyte ◽

Leishmania Species ◽

Hla Polymorphism ◽

Common Amino Acid ◽

Binding Core ◽

Epitope Discovery ◽

Epitope Binding ◽

The Impact

Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple Leishmania species. Epitopes binding to protection-associated HLA-DRB1 alleles shared common binding core motifs, mapping to the identified HLA-DRB1 amino acid polymorphisms. These results strongly suggest that HLA polymorphism, resulting in differential antigen presentation, affects the association between HLA and leishmaniasis disease development. Finally, we established a valuable open-access resource of putative epitopes. A set of 14 HLA-unrestricted strong-binding epitopes, conserved across species, was prioritized for further epitope discovery in the search for novel subunit-based vaccines.

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Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽

10.1093/genetics/149.1.445 ◽

1998 ◽

Vol 149 (1) ◽

pp. 445-458 ◽

Cited By ~ 21

Author(s):

Nick Goldman ◽

Jeffrey L Thorne ◽

David T Jones

Keyword(s):

Amino Acid ◽

Secondary Structure ◽

Protein Evolution ◽

Solvent Accessibility ◽

Strong Association ◽

Length Distribution ◽

Parametric Bootstrap ◽

Amino Acid Replacement ◽

Physical Constraints ◽

The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

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Ethanol/Gasoline Blends as Alternative Fuel in Last Generation Spark-Ignition Engines: A Review on CO and HC Engine Out Emissions

Energies ◽

10.3390/en14134034 ◽

2021 ◽

Vol 14 (13) ◽

pp. 4034

Author(s):

Paolo Iodice ◽

Massimo Cardone

Keyword(s):

Physicochemical Properties ◽

Alternative Fuels ◽

Experimental Studies ◽

Alternative Fuel ◽

Exhaust Emissions ◽

Spark Ignition ◽

Operating Conditions ◽

Spark Ignition Engine ◽

Spark Ignition Engines ◽

The Impact

Among the alternative fuels existing for spark-ignition engines, ethanol is considered worldwide as an important renewable fuel when mixed with pure gasoline because of its favorable physicochemical properties. An in-depth and updated investigation on the issue of CO and HC engine out emissions related to use of ethanol/gasoline fuels in spark-ignition engines is therefore necessary. Starting from our experimental studies on engine out emissions of a last generation spark-ignition engine fueled with ethanol/gasoline fuels, the aim of this new investigation is to offer a complete literature review on the present state of ethanol combustion in last generation spark-ignition engines under real working conditions to clarify the possible change in CO and HC emissions. In the first section of this paper, a comparison between physicochemical properties of ethanol and gasoline is examined to assess the practicability of using ethanol as an alternative fuel for spark-ignition engines and to investigate the effect on engine out emissions and combustion efficiency. In the next section, this article focuses on the impact of ethanol/gasoline fuels on CO and HC formation. Many studies related to combustion characteristics and exhaust emissions in spark-ignition engines fueled with ethanol/gasoline fuels are thus discussed in detail. Most of these experimental investigations conclude that the addition of ethanol with gasoline fuel mixtures can really decrease the CO and HC exhaust emissions of last generation spark-ignition engines in several operating conditions.

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Relationships Linking the Colour and Elemental Concentrations of Blossom Honeys with Their Antioxidant Activity: A Chemometric Approach

Agriculture ◽

10.3390/agriculture11080702 ◽

2021 ◽

Vol 11 (8) ◽

pp. 702

Author(s):

Monika Kędzierska-Matysek ◽

Anna Teter ◽

Małgorzata Stryjecka ◽

Piotr Skałecki ◽

Piotr Domaradzki ◽

...

Keyword(s):

Antioxidant Activity ◽

Physicochemical Properties ◽

Black Locust ◽

Antioxidant Properties ◽

Principal Component ◽

Botanical Origin ◽

Antioxidant Parameters ◽

Colour Parameters ◽

Hue Angle ◽

Chemometric Approach

The antioxidant activity of honey depends on the botanical origin, which also determines their physicochemical properties. In this study, a multivariate analysis was used to confirm potential relationships between the antioxidant properties and colour parameters, as well as the content of seven elements in five types of artisanal honey (rapeseed, buckwheat, linden, black locust, and multifloral). The type of honey was found to significantly influence most of its physicochemical properties, colour parameters, and the content of potassium, manganese and copper. Antioxidant parameters were shown to be significantly positively correlated with redness and concentrations of copper and manganese, but negatively correlated with the hue angle and lightness. The principal component analysis confirmed that the darkest buckwheat honey had the highest antioxidant activity in combination with its specific colour parameters and content of antioxidant minerals (manganese, copper and zinc). The level of these parameters can be potentially used for the identification of buckwheat honey.

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