Molecular Recognition by Pillar[5]arenes: Evidence for Simultaneous Electrostatic and Hydrophobic Interactions

 Pharmaceutics 2022, 14(1), 60

The formation of inclusion complexes between alkylsulfonate guests and a cationic pillar[5]arene receptor in water was investigated by NMR and ITC techniques. The results show the formation of host-guest complexes stabilized by electrostatic interactions and hydrophobic effects with binding constants for the guest with higher hydrophobic character. Structurally, the alkyl chain of the guest is included in the hydrophobic aromatic cavity of the macrocycle while the sulfonate groups are held in the multicationic portal by ionic interactions.

Delineation of molecular interactions of plant growth promoting bacteria induced β-1,3-glucanases and guanosine triphosphate ligand for antifungal response in rice: a molecular dynamics approach

Mol Biol Rep 49, 2579–2589 (2022)

Background

The plant growth is influenced by multiple interactions with biotic (microbial) and abiotic components in their surroundings. These microbial interactions have both positive and negative effects on plant. Plant growth promoting bacterial (PGPR) interaction could result in positive growth under normal as well as in stress conditions.

Methods

Here, we have screened two PGPR’s and determined their potential in induction of specific gene in host plant to overcome the adverse effect of biotic stress caused by Magnaporthe grisea, a fungal pathogen that cause blast in rice. We demonstrated the glucanase protein mode of action by performing comparative modeling and molecular docking of guanosine triphosphate (GTP) ligand with the protein. Besides, molecular dynamic simulations have been performed to understand the behavior of the glucanase-GTP complex.

Results

The results clearly showed that selected PGPR was better able to induce modification in host plant at morphological, biochemical, physiological and molecular level by activating the expression of β-1,3-glucanases gene in infected host plant. The docking results indicated that Tyr75, Arg256, Gly258, and Ser223 of glucanase formed four crucial hydrogen bonds with the GTP, while, only Val220 found to form hydrophobic contact with ligand.

Conclusions

The PGPR able to induce β-1,3-glucanases gene in host plant upon pathogenic interaction and β-1,3-glucanases form complex with GTP by hydrophilic interaction for induction of defense cascade for acquiring resistance against Magnaporthe grisea.

Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

 Molecular Biology Reports 49, 2129–2140 (2022)

Background

The genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers.

Methods and results

A total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean.

Conclusion

In the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar’s pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

Machine Learning Applied to the Oxygen-18 Isotopic Composition, Salinity and Temperature/Potential Temperature in the Mediterranean Sea

 Mathematics 2021, 9(19), 2523

This study proposed different techniques to estimate the isotope composition (δ18O), salinity and temperature/potential temperature in the Mediterranean Sea using five different variables: (i–ii) geographic coordinates (Longitude, Latitude), (iii) year, (iv) month and (v) depth. Three kinds of models based on artificial neural network (ANN), random forest (RF) and support vector machine (SVM) were developed. According to the results, the random forest models presents the best prediction accuracy for the querying phase and can be used to predict the isotope composition (mean absolute percentage error (MAPE) around 4.98%), salinity (MAPE below 0.20%) and temperature (MAPE around 2.44%). These models could be useful for research works that require the use of past data for these variables.

Production of a Potentially Probiotic Product for Animal Feed and Evaluation of Some of Its Probiotic Properties

 Int. J. Mol. Sci. 2021, 22(18), 10004

Nowadays, probiotics have been proposed for substituting antibiotics in animal feed since the European Union banned the latter compounds in 2006 to avoid serious side effects on human health. Therefore, this work aimed to produce a probiotic product for use in animal feed by fed-batch fermentation of whey with a combination of kefir grains, AGK1, and the fermented whole milk used to activate these kefir grains. The probiotic culture obtained was characterized by high levels of biomass (8.03 g/L), total viability (3.6 × 108 CFU/mL) and antibacterial activity (28.26 Activity Units/mL). Some probiotic properties of the probiotic culture were investigated in vitro, including its survival at low pH values, under simulated gastrointestinal conditions, after freezing in skim milk at −20 °C, and in the commercial feed during storage at room temperature. The viable cells of lactic and acetic acid bacteria and yeasts exhibited higher tolerance to acidic pH and simulated gastrointestinal conditions when the cells were protected with skim milk and piglet feed, compared with washed cells. The results indicated the feasibility of producing a probiotic product at a low cost with a potential application in animal feed.

Metal and metalloid profile as a fingerprint for traceability of wines under any Galician protected designation of origin

 Journal of Food Composition and Analysis, 102, 104043, 2021

Effective and cheap methods for detecting fraud and, guaranteeing wine authenticity, are of paramount importance in the sector. In this sense, three different kinds of prediction models (random forest, artificial neural networks, and support vector machines) were developed to classify wines, according to their element contents (metals and metalloids, obtained using an inductively coupled plasma with a quadrupole mass spectrometer, and an optic emission spectrophotometer). One models were developed using 45 inputs variables, and then the models were subjected to a process of reducing variables to simplify models and save material and time costs. A total accuracy was reached in all phases for the white wines-random forest models. From a practical point of view, the accuracy and the errors obtained by the selected models (except for red wines-artificial neural network developed using reduced variables) are acceptable. The models developed with fewer variables, can make the prediction task easier.

Modelling and Prediction of Monthly Global Irradiation Using Different Prediction Models

 Energies 2021, 14(8), 2332

Different prediction models (multiple linear regression, vector support machines, artificial neural networks and random forests) are applied to model the monthly global irradiation (MGI) from different input variables (latitude, longitude and altitude of meteorological station, month, average temperatures, among others) of different areas of Galicia (Spain). The models were trained, validated and queried using data from three stations, and each best model was checked in two independent stations. The results obtained confirmed that the best methodology is the ANN model which presents the lowest RMSE value in the validation and querying phases 1226 kJ/(m2∙day) and 1136 kJ/(m2∙day), respectively, and predict conveniently for independent stations, 2013 kJ/(m2∙day) and 2094 kJ/(m2∙day), respectively. Given the good results obtained, it is convenient to continue with the design of artificial neural networks applied to the analysis of monthly global irradiation.

Assessment of Glyphosate Impact on the Agrofood Ecosystem

 Plants 2021, 10(2), 405

Agro-industries should adopt effective strategies to use agrochemicals such as glyphosate herbicides cautiously in order to protect public health. This entails careful testing and risk assessment of available choices, and also educating farmers and users with mitigation strategies in ecosystem protection and sustainable development. The key to success in this endeavour is using scientific research on biological pest control, organic farming and regulatory control, etc., for new developments in food production and safety, and for environmental protection. Education and research is of paramount importance for food and nutrition security in the shadow of climate change, and their consequences in food production and consumption safety and sustainability. This review, therefore, diagnoses on the use of glyphosate and the associated development of glyphosate-resistant weeds. It also deals with the risk assessment on human health of glyphosate formulations through environment and dietary exposures based on the impact of glyphosate and its metabolite AMPA—(aminomethyl)phosphonic acid—on water and food. All this to setup further conclusions and recommendations on the regulated use of glyphosate and how to mitigate the adverse effects.

Main Applications of Cyclodextrins in the Food Industry as the Compounds of Choice to Form Host–Guest Complexes

 Int. J. Mol. Sci. 2021, 22(3), 1339

Cyclodextrins (CDs) are cyclic oligomers broadly used in food manufacturing as food additives for different purposes, e.g., to improve sensorial qualities, shelf life, and sequestration of components. In this review, the latest advancements of their applications along with the characteristics of the uses of the different CDs (α, β, γ and their derivatives) were reviewed. Their beneficial effects can be achieved by mixing small amounts of CDs with the target material to be stabilized. Essentially, they have the capacity to form stable inclusion complexes with sensitive lipophilic nutrients and constituents of flavor and taste. Their toxicity has been also studied, showing that CDs are innocuous in oral administration. A review of the current legislation was also carried out, showing a general trend towards a wider acceptance of CDs as food additives. Suitable and cost-effective procedures for the manufacture of CDs have progressed, and nowadays it is possible to obtain realistic prices and used them in foods. Therefore, CDs have a promising future due to consumer demand for healthy and functional products. 

Enhancing the saccharification of pretreated chestnut burrs to produce bacteriocins

 Journal of Biotechnology, 329, 13-20

The present study aims to valorize chestnut burrs, an important lignocellulosic waste, through a biorefinery concept. A solid residue rich in glucan (41.36 ± 0.59 %) and lignin (39.06 ± 0.01 %) obtained from a previous process of pre-hydrolysis was subjected to four treatments with water or NaOH to enhance enzymatic hydrolysis. Saccharification was performed using different ratios of commercial cellulases and β-glucosidases and at controlled pH 4.8 or 6.0 (with citrate buffer) or uncontrolled pH. Carbohydrate-rich solutions with or without nutrients were used to produce bacteriocins by Lactobacillus plantarum CECT 211. The use of NaOH at high temperatures (120 and 130 °C) was the most suitable treatment to improve saccharification. Regarding the production of bacteriocins, the best result was obtained using the enzymatic solution obtained at controlled pH 6.0, supplemented with MRS broth nutrients (except glucose). Thus, the concentrations of bacteriocins obtained in this culture medium (9.21 BU/mL) was 1.22 and 1.98 times higher than those obtained in the nutrient supplemented medium buffered at pH 4.8 (7.56 BU/mL) and in the commercial MRS broth (4.65 BU/mL), respectively. These results highlight the feasibility of the technology developed in this work.

Essential Oils as Antimicrobials in Crop Protection

 Antibiotics 2021, 10(1), 34

At present, organic crops have reached an important boom in a society increasingly interested in the conservation of the environment and sustainability. It is evident that a part of the population in the Western world focuses their concern on how to obtain our food and on doing it in a way that is as respectful as possible with the environment. In this review, we present a compilation of the work carried out with the use of essential oils as an alternative in the fight against different bacteria and fungi that attack crops and related products. Given the collected works, the efficacy of essential oils for their use as pesticides for agricultural use is evident.