Differentiation of Pathogenic Clinical Isolates and Laboratory Strains of Bacillus cereus by NMR-Based Metabolomics Analysis (2023)

In order to meet the food demands of a growing global population, agricultural productivity needs to be increased. In the early days, heavy use of chemical fertilizers and pesticides increased crop yields and resulted in severe environmental stress; however, these practices cannot continue and we must switch to using more environmentally friendly practices. The main obstacle to increasing food production is abiotic stress. Among abiotic stresses, water scarcity conditions, salinity, heat waves, excess water (floods), heavy rains and frost hinder agricultural productivity worldwide. Among the main alternatives to chemical fertilizers, microorganisms are already present in nature, where they act as growth stimulants for plant growth and also contribute to the mitigation of abiotic and biotic stresses. Microorganisms affect soil properties through the production of exopolysaccharides and the formation of biofilms. These properties of microbes have major implications for sustainable agriculture. Using a variety of microorganisms, it is possible to solve the current world food shortage problem. Our aim is to compile progress made in understanding stress mitigation mechanisms in crop plants to translate them into higher productivity. Multi-omics strategies describing plant-microbe interactions yield a wealth of information that helps determine what is happening inside cells in real time. In addition, we further demonstrate future pathways for rhizosphere microbes in sustainable agricultural production.

Under ongoing climate change and existing environments, plants are exposed to multiple adverse factors such as temperature extremes, high salinity, heavy metals (HMs), drought, and pathogens. Prolonged exposure to such adverse conditions can lead to phytotoxicity and overall delay in growth and development. Excess of HMs is one of the important factors that significantly affect plant growth. Plants have developed multiple defense mechanisms at the cellular and physiological levels to resist HMs stress. However, these internal defense mechanisms are insufficient to overcome excessive HMs stress. Plants produce various secondary messengers to activate cellular signaling, thereby activating several transcriptional responses related to plant defense. Different transcription factor (TF) gene families such as WRKY, my elob lastosis (MYB), basic leucine zipper domain (bZIP), basic helix-loop-helix (bHLH), APETALA2/ethylene response element binding protein (AP2/EREBP), Cys2-His2 (C2H2), receptor genes/proteins and kinases, such as mitogen-activated protein kinase (MAPK), play an important role in stress regulation using hormone-mediated pathways under HMs stress effect. In addition, phytohormones and their signaling networks also contribute to modulating cellular functions at the molecular level against HMs stress. Several mechanisms have been explored to understand plant defense mechanisms under HMs stress. However, many more advanced molecular approaches are needed to explore these defense mechanisms. Here, we describe how OMICS improve plant internal defenses to counteract HMs stress.

Heat and acidic electrolyzed water (AEW) are believed to be effective in inactivating microorganisms. Although a previous study demonstrated that theirListeria harmlessthrough metabolomicsin vitro, the basic mechanism of inactionListeria monocytogenesLittle is known about the use of this approach in food systems. This work identified the surviving population and injuries of three individualsListeria monocytogenesStrains (SSA81, LM44 and LM3) were inoculated alone or in combination on salmon under heat (60°C) and AEW (100mg/L available free chlorine, pH 2.42, redox potential 1182mV) treatments. Bactericidal mechanisms were explored using nuclear magnetic resonance (NMR) and multivariate data analysis. Our results showed that heat treatment and AEW treatment alone resulted in 0.4 and 1.2 log CFU/g reductionListeria monocytogenes, respectively. Combined heat treatment and AEW resulted in a significant reduction of 2.1–2.2 log CFU/gListeria monocytogenes.over 25%, 35% and 55% damageListeria monocytogenesObserved under heat, AEW, and combined treatments, respectively. Overall, 43 metabolites were characterized in the three strains. Short-term heating may activate cellular protective systems by accumulating amino and organic acids. AEW leads to decreased metabolites due to oxidative stress and acid stress. In combined treatment, AEW plays a major role, and its bactericidal ability is enhanced by heat. Under the synergistic stress of heat and AEW, significant decreases in Val, Leu, Tyr and Trp were detected in all strains (P<0.05). Under the combined treatment of SSA81, LM44 and LM3, 15, 7 and 6 pathways were significantly changed, respectively, mainly including amino acid, energy and carbohydrate metabolism. Strain LM3 exhibited the strongest resistance to oxidative stress by enhancing the Glu decarboxylase system, whereas this compensatory pathway was attenuated in SSA81 and LM44. These findings suggest that the bactericidal mechanism can be well explained by interference pathways.

Organic acids secreted by phosphate-solubilizing bacteria (PSBs) are one of the major biological metabolites that have the ability to mobilize cadmium (Cd) when converting insoluble precipitate forms to bioavailable forms in contaminated soils. However, fluctuations in nutrient element concentration caused by agricultural activities may lead to significant differences in carbohydrate metabolism of microorganisms involved in Cd repair, so it is necessary to study how metabolic strategies, especially organic acids, are affected by environmentally friendly fertilizers, such as potassium (K) . In this study, adding K⁺Concentrations of (KCl) from 0.0 to 100.0 mg/L in the medium significantly accelerated Cd mobilization by inducing the secretion of tartaric acid, 3-hydroxybutyric acid, fumaric acid and succinic acid. 4.3- and 4.1-fold changes, respectively. The present data suggest that significant differences in metabolic pathways and gene expression are associated with different K⁺Concentrations include: Ⅰ) K⁺induced a significant upregulation of the metabolic pathways from pyruvate to oxaloacetate and tartrate; ii) differential expression of genes involved in encoding Krebs cycle enzymes resulted in an upregulation of fumarate, succinate and 3-hydroxybutyrate; iii) subsequent As the concentration of bioavailable Cd increased, the expression of enzyme genes related to cysteine ​​and glutamate metabolism increased. In addition, P-type ATPase activity increased with K⁺level, indicating that H⁺Outflow and medium acidification are enhanced. In general, appropriate application of potassium fertilizer is an effective way to restore soil Cd by regulating organic acid metabolism and H+.⁺Secretion of PSBs.

With the implementation of major scientific programs such as the Human Genome Project, genomics, transcriptomics and proteomics have played an important role in human life science research. At the same time, metabolomics came into being and developed rapidly since the mid-1990s. Together with genomics, transcriptomics and proteomics it forms systems biology. Genomics, transcriptomics, proteomics and metabolomics play an integral role in the life sciences. They conduct research on different levels of regulating the life process, enabling people to study life phenomena at the molecular level, explore the essence of life, and gradually and systematically understand the laws of life development. Together with bioinformatics, these methods form an important part of systems biology. Metabolomics studies all metabolic responses of individuals to stimuli, environmental changes and genetic modifications of exogenous substances (drugs or poisons) and examines the overall picture and dynamics of these responses. Metabolomics provides powerful modern experimental technology for the development of life sciences, and also provides new technical support and guarantee for the preclinical safety evaluation and practice of new drugs. The emergence of metabolomics makes up for the lack of microscopic research such as genomics and proteomics. As analytical methods and data analysis improve, all information about an organism obtained by metabolomics will be interpreted comprehensively. Through the analysis of this large amount of information, the biomarkers that are found to be drug or clinically relevant are metabolites. It is believed that metabolomics is playing an increasingly important role in clinical practice and in the development of new drugs.

Soils contaminated with toxic metals and metalloids pose a serious threat to agricultural production around the world. With the rapid expansion of industrialization and urbanization, harmful substances are being released freely into the atmosphere, resulting in increased soil and air pollution. In addition, deforestation is another important factor that increases the accumulation of toxic waste in the air and soil. Avoiding and mitigating the effects of soil pollution is an important challenge. The ability of plants to transform, transfer and reduce the harmful effects of heavy metals and metalloids can be significantly improved through genetic engineering. Utilizing efficient gene transfer pathways, there is great potential for breeding metal-tolerant plants. In this chapter, we discuss modern methods of genetically engineering plants to enhance phytoremediation capabilities from the perspective of metal and metalloid tolerance. An important assessment of methods for developing plants that can effectively remediate soils and increase tolerance to extreme metal stress. Advanced methods for the genetic engineering of metal-tolerant plants are also described. Furthermore, promising directions for overcoming the shortcomings of phytoremediation through genetic engineering strategies are also predicted. The information gathered here may help in the planning of new experimental studies aimed at increasing plant tolerance to heavy metals and metalloids. In addition, genome editing is an emerging strategy that can be used to improve the ability of plants to perform effective phytoremediation of toxic substances. Furthermore, we highlight advanced approaches, including omics and genome editing, to enhance phytoremediation and metal stress tolerance, and highlight their innovative, practical, and future applications in safe and sustainable agriculture.

Journal of Molecular Graphics and Modeling, Vol. 71, 2017, Pages 154-166

Protein kinases (PKs), a class of serine/threonine kinases (STKs), are important drug targets for the treatment of various human diseases. Among protein kinases, casein kinases (CKs) are abundantly expanded in various organisms, among them, the malaria parasitePlasmodium falciparumhas a member, namelyPfCKI, which can phosphorylate various proteins in parasite extractsin vitroHealth status. However, the structure-function relationshipPfThe dynamics of CKI and ATP binding remain to be understood. Since then, attempts have been made to study its kinetics, stability, and ATP-binding mechanism.PfCKI through computational modeling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. bilobal catalytic domainPfCKI shares a high degree of secondary structure topology with CKI domains from rice, human, and mouse, suggesting co-evolution of these kinases. Molecular docking studies revealed that ATP binds to the active site, where a glycine-rich ATP-binding motif (G16-X-G18-X-X-G21) along with a small number of conserved residues plays a critical role in maintaining complex stability effect. superposition of structuresPfCKIs with close structural homologues describe important loops that differ in position and length, indicating the dynamic nature of these loops among CKIs, which is consistent with principal component analysis (PCA). PCA showed that the overall global motion of the ATP-bound form was relatively higher than that of the apo form. This study provides insights into structural featuresPfCKI, which will contribute to further understanding of the associated protein structures, catalytic kinetics, and phosphorylation mechanisms of these important STKs from malaria parasites in the near future.

Journal of Photochemistry and Photobiology A: Chemistry, Vol. 358, 2018, pp. 111-120

In this study, optimization of the photocatalytic degradation of simulated textile wastewater containing two pollutants, methylene blue (MB) and zinc, consisted of studying the variation of four parameters, the initial MB concentration ([MB]_I, mg/L), zinc concentration ([Zn²⁺]_I, mg/L), sodium chloride concentration ([NaCl]_I, M) and flow rate (Q, mL/min) by experimental design using response surface methodology. The results show that the order of importance for MB degradation depends on NaCl concentration > MB concentration > ionized zinc concentration > flow rate. The modeling results show that there is good agreement between the predicted value and the experimental value, and the correlation coefficient is acceptable (R²=0.9879 and R²(adjusted) = 0.9773). Apply the desirability function to a second-order polynomial equation to determine the optimal experimental conditions for the fastest total photocatalytic degradation, determined as follows: For a maximum target of 85.91% and a desirability of d = 1.0, [MB] = 75mg/L, [zinc²⁺]=45mg/L, [NaCl]=0.125M, Q=500mL/min. In addition, the results show that zinc has a good affinity for cellulosic materials, which helps to enhance the activity in terms of photocatalytic degradation. Optimal conditions for dye mineralization were assessed using the TOC method. In addition, special attention was paid to better understanding the impact of inorganic contaminants and the scavenging effects of different molecules such as EDTA, isopropanol and CCl₄Reviewed and discussed.

Separation and Purification Technology, Volume 176, 2017, Pages 145-158

The use of silver in consumer products and its subsequent leaching in gray water shows an increasing trend. Not only is silver recycling commercially profitable, but it is also necessary for the environment. trace silver⁺and high concentrations of other competing cations (Na⁺, calcium²⁺, magnesium²⁺) in typical laundry wash water makes the separation process challenging. Due to its high selectivity for silver, the use of ion exchange resins with thiol groups in the chain offers a potential solution. This work successfully recovered silver (>90%) to high-purity grade Ag₂S powder (>99%) was obtained from an aqueous solution of synthetic ash using a commercially available resin, Ambersep GT74, in fixed-bed column mode. The regeneration process at work has been optimized for solution pH and thiourea concentration (0.5M thiourea concentration at pH 1). Resin and regenerant have been used in multiple cycles (4 times) without affecting its performance. The study successfully demonstrates a closed-loop sustainable scenario where no chemicals/toxics are released into the environment by reusing and recycling all raw materials until exhausted.

Indian Armed Forces Medical Journal, Vol. 71, No. 1, 2015, Pages 43-47

Food Control, Volume 60, 2016, Pages 302-308

A SYBR Green-based real-time PCR (qPCR) procedure for the rapid and specific detection of enterotoxin productionstaphylococcusThe genus has been developed in meat products. To this end, specific primer pairs based on conserved regions of enterotoxin genes were designed to detect most of the staphylococcal enterotoxins described. Does not cross-react with other microorganisms or produce enterotoxinsstaphylococcusis detected. After an 8-hour enrichment period at 30°C, the detection limit was approximately 2–40 cfu/g for artificially contaminated meat products. The total time to complete the assay is approximately 12 hours. Therefore, the qPCR method provides a useful, rapid and efficient tool to screen for enterotoxigenicstaphylococcusin meat products. This tool can also be used to monitor for these foodborne pathogens in food safety prevention programs.

Chemosphere, Vol. 195, 2018, pp. 847-853

Despite growing interest in natural catalyst-based Fenton oxidation processes, the use of laterite soils to facilitate sequential adsorption/oxidation processes of fluoroquinolone antibiotics has been rarely investigated. In this work, the ability of African red soils containing goethite and hematite to remove flumequine (FLU), a representative compound of fluoroquinolone antibiotics, was assessed under dark and UVA irradiation. Batch experiments and liquid chromatography analysis indicated that the presence of laterite could enhance FLU removal in heavily polluted water (up to 94% of 77 μmol L⁻¹FLU and 72% mineralization). Heterogeneous reaction rates determined by intrinsic surface chemical reaction rates, including adsorption and oxidation of FLU, and photoinduced reduction of Fe^threesite of iron production^two. Based on probe and clear experiments,OH radicals mainly participate in heterogeneous oxidation reactions. The light-assisted Fenton process efficiently removes FLU even in the presence of a second fluoroquinolone antibiotic, norfloxacin (NOR), which can be co-found with FLU in the affected environment. Determination of kinetic rate constants and total organic carbon (TOC) for five consecutive adsorption/oxidation cycles revealed that laterites exhibit no deactivation of surface sites and excellent catalytic stability. This cost-effective and environmentally friendly remediation technique may become a promising approach for the removal of fluoroquinolone antibiotics from multi-polluted waters.