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Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples

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A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Natural and Bio-derived Molecules".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 27031

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Dr. Maroula Kokotou

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Laboratory of Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
Interests: mass spectrometry; liquid chromatography–high resolution mass spectrometry (LC-HRMS); lipidomics; bioactive food ingredients; study of organic reaction mechanisms by HRMS
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Prof. Dr. Petros Tarantilis

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Laboratory of Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
Interests: isolation, purification, and structure determination of natural products using chromatographic and spectroscopic techniques; study of biological activity of natural products; instrumental methods of plants and food analysis; development of methods for quality determination, adulteration, and authenticity (botanical and geographical origin) of food
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Dr. Christos Pappas

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Laboratory of Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
Interests: instrumental chemical analysis of natural products (chromatographic and spectroscopic techniques); isolation, purification, and structure determination of natural products using chromatographic and spectroscopic techniques; development of new techniques for separation, evaluation, and chemical analysis of main compounds of plants cultivated in Greece; development of methods based on spectroscopic techniques (FT-IR, Raman) and chemometrics for differentiation natural products and microorganisms; food authenticity
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Dear Colleagues,

Small organic biomolecules contained in foods or derived from plants (natural products) are increasingly being recognized as biomolecules able to regulate and control cellular function. It is widely accepted that various foods and plant extracts are associated with effects against diseases, such as metabolic and cardiovascular diseases and cancer, due to the presence of bioactive primary and secondary metabolites. For example, polyphenols are plant secondary metabolites ubiquitous in fruits, vegetables, and cereals, which have been associated positively with numerous health benefits. Lipids constitute another example of small biomolecules, which may play a role in the protection and promotion of human health. Although the exact mechanisms of action of the food ingredients are mostly unclear and under continuous investigation, there is a great demand for analytical methods for the sensitive and precise determination of small bioactive molecules in food, plant, and biological samples.

Analytical approaches employing mass spectrometry (MS) have been recognized as a powerful and rapidly growing technology that can be used in biomedical and natural product research not only to identify novel bioactive small molecules, but also to study disease mechanisms. MS combined with either liquid chromatography (LC-MS) or gas chromatography (GC-MS) is the major technique used for the detection and determination of small bioactive molecules in various matrices. In particular, high-resolution mass spectrometry (HRMS) offers the high sensitivity and high mass accuracy required for the detection and quantification of low abundance small biomolecule species. Fourier transform infrared (FTIR) and Raman spectroscopy are complementary techniques for the analysis of small biomolecules. The aim of the present Special Issue is to compile review articles and original research articles covering recent advances in the analysis of small bioactive molecules (primary and secondary metabolites) in foods, plants, and biological samples.

Dr. Maroula Kokotou
Prof. Dr. Petros Tarantilis
Dr. Christos Pappas
Guest Editors

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

Bioactive food ingredients (primary and secondary metabolites)
Secondary metabolites—natural products
Liquid chromatography–mass spectrometry
Fourier transform infrared (FTIR) and Raman spectroscopic analysis
Gas chromatography–mass spectrometry
High-resolution mass spectrometry
Lipids—amino acids—carbohydrates
Polyphenols–terpenes

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Related Special Issue

Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples, Volume II in Biomolecules (1 article)

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Research

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15 pages, 1852 KiB

Open AccessArticle

Chemical Composition of the Essential Oils of Three Popular Sideritis Species Cultivated in Greece Using GC-MS Analysis

by Eleftheria H. Kaparakou, Dimitra Daferera, Charalabos D. Kanakis, Efstathia Skotti, Maroula G. Kokotou and Petros A. Tarantilis

Biomolecules 2023, 13(7), 1157; https://doi.org/10.3390/biom13071157 - 20 Jul 2023

Cited by 6 | Viewed by 2352

Abstract

(1) Background: The essential oils (EOs) of Sideritis L. have attracted great interest due to their pharmacological activities and potential applications in the cosmetic and perfume industries. The aim of this work was to study the EO chemical composition of three of the most popular, in Greece, mountain tea species: namely, these include Sideritis scardica, Sideritis raeseri, and Sideritis syriaca. (2) Methods: The EOs were obtained from the aerial parts of three Sideritis species that were cultivated in various regions of Greece by hydrodistillation, and the chemical composition was studied by gas chromatography–mass spectrometry (GC-MS) analysis. (3) Results: The EOs of the Sideritis species—S. scardica (SSC1, SSC2, SSC3), S. raeseri (SR1, SR2, SR3), and S. syriaca (SS1, SS2, SS3)—were analyzed by GC-MS, and they showed both qualitatively and quantitatively high variation in their chemical composition. (4) Conclusions: The EOs of S. scardica and S. raeseri from three different regions of Greece, and the S. syriaca from three different localities of Crete Island in Southern Greece, showed high chemical variability. Although 165 different components were found to be present in the nine samples through GC-MS analysis, only 7 (1-octen-3-ol, linalool, trans-pinocarveol, p-mentha-1,5-dien-8-ol, α-terpineol, myrtenol, and verbenone) were common components in the nine EOs, which were identified to be highly variable in different percentages among the samples. Even the EOs of SS1 and SS2, which were cultivated nearby, showed different GC profiles. The composition variation observed might be attributed to differentiations in the soil and climatic conditions. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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12 pages, 3126 KiB

Open AccessCommunication

Targeted and Suspect Fatty Acid Profiling of Royal Jelly by Liquid Chromatography—High Resolution Mass Spectrometry

by Christiana Mantzourani and Maroula G. Kokotou

Biomolecules 2023, 13(3), 424; https://doi.org/10.3390/biom13030424 - 23 Feb 2023

Cited by 2 | Viewed by 1731

Abstract

Royal jelly (RJ) is a bee product produced by the mandibular and hypopharyngeal glands of worker honeybees which has attracted special attention because of its numerous pharmacological activities and its applications to dermatology and cosmetics. In 2020, we demonstrated a liquid chromatography–high resolution mass spectrometry (LC–HRMS) method for the determination of seven medium-chain FFAs in RJ samples. The aim of the present work was to extend our studies on FA profiling of RJ, exploring the presence of common long-chain saturated, mono-unsaturated and poly-unsaturated free FAs in RJ samples using this LC–HRMS method. Among twenty common FAs studied by a targeted approach, palmitic acid, stearic acid and oleic acid were found at concentrations higher than the rest of the FAs (the concentrations of these three acids ranged from 37.4 to 48.0, from 17.7 to 24.0 and from 9.4 to 11.1 mg/100 g of fresh RJ, respectively). The high mass accuracy of LC–HRMS allowed the application of a suspect approach, which enabled the exploration of various C9 and C11 FAs, as well as hydroxylated C12 FAs. Nonenoic acid was indicated as the most abundant among these acids. In addition, for the first time, the presence of a variety of regio-isomers of hydroxymyristic, hydroxypalmitic and hydroxystearic acids was demonstrated in RJ samples. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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11 pages, 947 KiB

Open AccessArticle

Taste Compounds and Polyphenolic Profile of Tomato Varieties Cultivated with Beneficial Microorganisms: A Chemical Investigation on Nutritional Properties and Sensory Qualities

by Carlo Francesco Morelli, Adele Cutignano, Giovanna Speranza, Gennaro Roberto Abbamondi, Marco Rabuffetti, Carmine Iodice, Rocco De Prisco and Giuseppina Tommonaro

Biomolecules 2023, 13(1), 117; https://doi.org/10.3390/biom13010117 - 6 Jan 2023

Cited by 2 | Viewed by 2481

Abstract

There is a strong need to develop eco-sustainable agricultural techniques to improve crop yields while preserving biomolecule contents and reducing the adverse environmental impact of agro-chemicals. The use of microorganisms in agriculture represents an attractive and innovative solution. Herein, a chemical study on the nutritional and sensory qualities of San Marzano Cirio 3 (SMC3), Corbarino (CO) and Brandywine (BW) tomato varieties cultivated with and without effective microorganisms (EM) is reported. LC–MS analysis of the methanolic extracts allowed for the identification of 21 polyphenol derivatives. In different proportions among the studied varieties, the two main polyphenols were rutin and naringenin chalcone; the latter was isolated and chemically identified by complementary HR-ESIMS/MS and NMR methods. SMC3 and CO were richer in naringenin chalcone. Conversely, BW showed higher proportions of rutin; however, in all cases, the relative amounts of the two polyphenols considered together increased over the other minor components after the EM treatment. The qualitative and quantitative HPLC analyses of taste-active compounds (aspartic acid, glutamic acid, AMP and GMP) revealed a significant difference in aspartic and glutamic acids and ribonucleotide contents according to the cultivation condition (±EM), particularly in BW. This study provides chemical data in support of the use of EM green technology for the cultivation of edible agricultural products, such as tomato preserves, and may even improve nutritional and sensory qualities while safeguarding the environment. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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18 pages, 1017 KiB

Open AccessArticle

Polar Phenol Detection in Plasma and Serum: Insights on Sample Pre-Treatment for LC/MS Analysis and Application on the Serum of Corinthian Currant-Fed Rats

by Paraskevi B. Vasilakopoulou, Aimilia-Tatiana Gousgouni, Amalia E. Yanni, Nikolaos Kostomitsopoulos, Vaios T. Karathanos and Antonia Chiou

Biomolecules 2022, 12(12), 1838; https://doi.org/10.3390/biom12121838 - 8 Dec 2022

Cited by 3 | Viewed by 1851

Abstract

Analysis of plasma and serum provides valuable information on the amounts of polar phenols’ circulating after ingestion. In the present study, protein precipitation (PPT), liquid–liquid extraction (LLE), solid phase extraction (SPE), enzymatic hydrolysis and their combinations were meticulously evaluated for the extraction of a variety of polar phenolic moieties from plasma and serum. The recovery values of the above methods were compared; satisfactory recoveries (>60%) were attained for most analytes. Polar phenol aglycones undergo degradation with enzymatic hydrolysis; however, their extended phase II metabolism makes enzymatic hydrolysis a mandated process for their analysis in such biofluids. Hence, enzymatic hydrolysis followed by LLE was used for the identification of polar phenols in rats’ serum, after the long-term oral consumption of Corinthian Currant. Corinthian Currant is a Greek dried vine product rich in bioactive polar phenolics. Flavonoids and phenolic acids, detected as aglycones, ranged from 0.57 ± 0.08 to 181.66 ± 48.95 and 3.45 ± 1.20 to 897.81 ± 173.96 ng/mL, respectively. The majority of polar phenolics were present as phase II metabolites, representing their fasting state in the blood stream. This is the first study evaluating the presence of polar phenolics in the serum of rats following a long-term diet supplemented with Corinthian Currant as a whole food. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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11 pages, 291 KiB

Open AccessArticle

Grape Pulp Fiber as Possible Fining Agents for Red Wine

by Andrea Osete-Alcaraz, Lucía Osete-Alcaraz, Ana Eugenia Ortega-Regules, Ana Belen Bautista-Ortín and Encarna Gómez-Plaza

Biomolecules 2022, 12(10), 1519; https://doi.org/10.3390/biom12101519 - 20 Oct 2022

Cited by 3 | Viewed by 2049

Abstract

One of the biggest problems with the use of traditional fining agents is that some of them present allergenic characteristics or are not suitable for vegan consumers due to their animal origin. An alternative to these traditional proteinaceous agents could be cell walls from grape pulp. This material could be used to modify the final phenolic concentration of a wine due to its affinity for phenolic compounds. In this study, the ability of freeze-dried grape pulp fiber, rich in pulp cell walls, to act as a fining agent was analyzed in wines from three different varieties: Cabernet Sauvignon, Syrah, and Monastrell. After the use of this material, the wine chromatic characteristics and total tannin concentration were analyzed by spectrophotometric and chromatographic techniques. In addition, the wines were contaminated with ochratoxin A and histamine to check whether this material could also be a tool for removing these wine contaminants. The pulp fiber presented a high capacity to retain phenolic compounds, especially tannins; however, there were differences depending on the studied wine. The largest reduction in tannin concentration after fining was observed when this material was used in Cabernet Sauvignon wines (23%), whereas for Monastrell wines the reduction was lower (18.3%) and even lower for Syrah wines (14.3%). This fining agent also reduced the anthocyanin concentration of the three red wines, although to a lesser extent than the reduction observed for tannins. A really interesting result was that the addition of this fining agent reduced the concentration of ochratoxin A by 50% in all the studied wines. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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20 pages, 4044 KiB

Open AccessArticle

Isolation and Characterization of 1-Hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic Acid, a Metabolite in Bacterial Transformation of Abscisic Acid

by Oleg S. Yuzikhin, Alexander I. Shaposhnikov, Tatyana A. Konnova, Darya S. Syrova, Hamza Hamo, Taras S. Ermekkaliev, Valerii P. Shevchenko, Konstantin V. Shevchenko, Natalia E. Gogoleva, Anton A. Nizhnikov, Vera I. Safronova, Alexander A. Kamnev, Andrey A. Belimov and Yuri V. Gogolev

Biomolecules 2022, 12(10), 1508; https://doi.org/10.3390/biom12101508 - 18 Oct 2022

Cited by 5 | Viewed by 2373

Abstract

We report the discovery of a new abscisic acid (ABA) metabolite, found in the course of a mass spectrometric study of ABA metabolism by the rhizosphere bacterium Rhodococcus sp. P1Y. Analogue of (+)-ABA, enriched in tritium in the cyclohexene moiety, was fed in bacterial cells, and extracts containing radioactive metabolites were purified and analyzed to determine their structure. We obtained mass spectral fragmentation patterns and nuclear magnetic resonance spectra of a new metabolite of ABA identified as 1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic acid, which we named rhodococcal acid (RA) and characterized using several other techniques. This metabolite is the second bacterial ABA degradation product in addition to dehydrovomifoliol that we described earlier. Taken together, these data reveal an unknown ABA catabolic pathway that begins with side chain disassembly, as opposed to the conversion of the cyclohexene moiety in plants. The role of ABA-utilizing bacteria in interactions with other microorganisms and plants is also discussed. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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16 pages, 2601 KiB

Open AccessArticle

Rapid Assessment of Lipidomics Sample Purity and Quantity Using Fourier-Transform Infrared Spectroscopy

by Harley Robinson, Jeffrey Molendijk, Alok K. Shah, Tony Rahman, Gregory J. Anderson and Michelle M. Hill

Biomolecules 2022, 12(9), 1265; https://doi.org/10.3390/biom12091265 - 8 Sep 2022

Cited by 3 | Viewed by 2463

Abstract

Despite the increasing popularity of liquid chromatography–mass spectrometry (LC-MS)-based lipidomics, there is a lack of accepted and validated methods for lipid extract quality and quantity assessment prior to LC-MS. Fourier-Transform Infrared Spectroscopy (FTIR) has been reported for quantification of pure lipids. However, the impact of complex lipid sample complexity and purity on total lipid quantification accuracy has not been investigated. Here, we report comprehensive assessment of the sample matrix on the accuracy of lipid quantification using Attenuated Total Reflectance (ATR)-FTIR and establish a simple workflow for lipidomics sample quantification. We show that both pure and complex lipids show characteristic FTIR vibrations of CH- and C=O-stretching vibrations, with a quantitative range of 40–3000 ng and a limit of detection of 12 ng, but sample extraction method and local baseline subtraction during FTIR spectral processing significantly impact lipid quantification via CH stretching. To facilitate sample quality screening, we developed the Lipid Quality (LiQ) score from a spectral library of common contaminants, using a ratio of peak heights between CH stretching vibrations maxima and the collective vibrations from amide/amine, CH-stretching minima and sugar moieties. Taking all tested parameters together, we propose a rapid FTIR workflow for routine lipidomics sample quality and quantity assessment and tested this workflow by comparing to the total LC-MS intensity of targeted lipidomics of 107 human plasma lipid extracts. Exclusion of poor-quality samples based on LiQ score improved the correlation between FTIR and LC-MS quantification. The uncertainty of absolute quantification by FTIR was estimated using a 795 ng SPLASH LipidoMix standard to be <10%. With low sample requirement, we anticipate this simple and rapid method will enhance lipidomics workflow by enabling accurate total lipid quantification and normalization of lipid quantity for MS analysis. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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15 pages, 6819 KiB

Open AccessEditor’s ChoiceArticle

Correlation of Serum Acylcarnitines with Clinical Presentation and Severity of Coronary Artery Disease

by Olga Deda, Eleftherios Panteris, Thomas Meikopoulos, Olga Begou, Thomai Mouskeftara, Efstratios Karagiannidis, Andreas S. Papazoglou, Georgios Sianos, Georgios Theodoridis and Helen Gika

Biomolecules 2022, 12(3), 354; https://doi.org/10.3390/biom12030354 - 23 Feb 2022

Cited by 19 | Viewed by 3136

Abstract

Recent studies support that acylcarnitines exert a significant role in cardiovascular disease development and progression. The aim of this metabolomics-based study was to investigate the association of serum acylcarnitine levels with coronary artery disease (CAD) severity, as assessed via SYNTAX Score. Within the context of the prospective CorLipid trial (NCT04580173), the levels of 13 circulating acylcarnitines were accurately determined through a newly developed HILIC-MS/MS method in 958 patients undergoing coronary angiography in the AHEPA University Hospital of Thessaloniki, Greece. Patients presenting with acute coronary syndrome had significantly lower median acylcarnitine C8, C10, C16, C18:1 and C18:2 values, compared to patients with chronic coronary syndrome (p = 0.012, 0.007, 0.018, 0.011 and <0.001, respectively). Among CAD subgroups, median C5 levels were significantly decreased in unstable angina compared to STEMI (p = 0.026), while median C10, C16, C18:1 and C18:2 levels were higher in stable angina compared to STEMI (p = 0.019 p = 0.012, p = 0.013 and p < 0.001, respectively). Moreover, median C2, C3, C4 and C8 levels were significantly elevated in patients with diabetes mellitus (p < 0.001, <0.001, 0.029 and 0.011, respectively). Moreover, short-chain acylcarnitine C2, C4, C5 and C6 levels were elevated in patients with heavier calcification and lower left ventricular ejection fraction (LVEF) % (all p-values less than 0.05). With regard to CAD severity, median C4 and C5 levels were elevated and C16 and C18:2 levels were reduced in the high CAD complexity group with SYNTAX Score > 22 (p = 0.002, 0.024, 0.044 and 0.012, respectively), indicating a potential prognostic capability of those metabolites and of the ratio C4/C18:2 for the prediction of CAD severity. In conclusion, serum acylcarnitines could serve as clinically useful biomarkers leading to a more individualized management of patients with CAD, once further clinically oriented metabolomics-based studies provide similar evidence. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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11 pages, 3579 KiB

Open AccessArticle

Volatile Emissions and Relative Attraction of the Fungal Symbionts of Tea Shot Hole Borer (Coleoptera: Curculionidae)

by Paul E. Kendra, Nurhayat Tabanca, Luisa F. Cruz, Octavio Menocal, Elena Q. Schnell and Daniel Carrillo

Biomolecules 2022, 12(1), 97; https://doi.org/10.3390/biom12010097 - 7 Jan 2022

Cited by 11 | Viewed by 2875

Abstract

Euwallacea perbrevis is an ambrosia beetle that vectors fungal pathogens causing Fusarium dieback in Florida avocado trees. Current monitoring lures contain quercivorol, a fungus-produced volatile, but the exact attractant is unknown since lures contain a mixture of p-menth-2-en-1-ol isomers and both α- and β-phellandrene. This study used pure cultures of six symbiotic fungi isolated from E. perbrevis to document volatile emissions and determine the relative attraction of symbionts in binary choice assays. In a comparative test, headspace solid-phase microextraction followed by gas chromatography–mass spectroscopy was used to identify and quantify emissions from 3-week-old cultures. In a temporal study, Super-Q collection followed by gas chromatography–flame ionization detection was used to measure cis- and trans-p-menth-2-en-1-ol emissions for three months. A total of 15 compounds were detected, with monoterpene hydrocarbons and oxygenated monoterpenoids predominating. Only trans-p-menth-2-en-1-ol was common to all six symbionts. Peak levels of both isomers were observed at day 7, then gradually declined over a 90 day period. In choice tests, avocado sawdust disks inoculated with Fusarium sp. nov. were the most attractive. This symbiont produced only two volatiles, trans-p-menth-2-en-1-ol and limonene. The combined results indicate that trans-p-menth-2-en-1-ol is the primary female attractant emitted from symbiotic fungi, but limonene may be a secondary attractant of E. perbrevis. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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Review

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16 pages, 620 KiB

Open AccessReview

The Influence of Biomolecule Composition on Colloidal Beer Structure

by Irina N. Gribkova, Michail N. Eliseev, Yuri D. Belkin, Maxim A. Zakharov and Olga A. Kosareva

Biomolecules 2022, 12(1), 24; https://doi.org/10.3390/biom12010024 - 24 Dec 2021

Cited by 6 | Viewed by 3640

Abstract

Recent studies have revealed an interest in the composition of beer biomolecules as a colloidal system and their influence on the formation of beer taste. The purpose of this research was to establish biochemical interactions between the biomolecules of plant-based raw materials of beer in order to understand the overall structure of beer as a complex system of bound biomolecules. Generally accepted methods of analytical research in the field of brewing, biochemistry and proteomics were used to solve the research objectives. The studies allowed us to establish the relationship between the grain and plant-based raw materials used, as well as the processing technologies and biomolecular profiles of beer. The qualitative profile of the distribution of protein compounds as a framework for the formation of a colloidal system and the role of carbohydrate dextrins and phenol compounds are given. This article provides information about the presence of biogenic compounds in the structure of beer that positively affect the functioning of the body. A critical assessment of the influence of some parameters on the completeness of beer taste by biomolecules is given. Conclusion: the conducted analytical studies allowed us to confirm the hypothesis about the nitrogen structure of beer and the relationship of other biomolecules with protein substances, and to identify the main factors affecting the distribution of biomolecules by fractions. Full article

(This article belongs to the Special Issue Cutting-Edge Research on the Analysis of Small Biomolecules in Foods, Plants, and Biological Samples)

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