Sugar-phosphate Research Articles

Targeted analysis of sugar phosphates from glycolysis pathway by phosphate methylation with liquid chromatography coupled to tandem mass spectrometry

Monitoring the glycolysis pathway remains an analytical challenge as most metabolites involved are sugar phosphates. Structural similarity, instability, high polarity, and rich negative charges of sugar phosphates make LC-MS based analysis challenging. Here, we developed an improved workflow integrating uniformly 13C-labeled yeast metabolite extract, TiO2-based enrichment, differential stable isotope labeling phosphate methylation, porous graphic carbon column, and selected reaction monitoring acquisition. Uniformly 13C labeled yeast metabolite extract was used as internal standards while differential stable isotope labeled sugar phosphates worked as calibrants. The established method was validated in human plasma, platelet and cultured HeLa cells. The limits of quantification ranged between 0.25 and 0.54 pmol on column. The method was adapted and its applicability tested for human platelets in which activation with collagen-related peptide (CRP) clearly showed the upregulation of some SPx metabolites. The results document that this newly established method can be successfully used to monitor glycolysis in different biological samples. As an extension, more phosphorylated and carboxylated metabolites from the central carbon metabolism (pentose phosphate cycle, TCA cycle) were tested as well. This method showed superior performance, especially for multiple phosphorylated and carboxylated metabolites. For quantitative purpose, the concept of SPx in three sets (12C-analytes, U-13C-IS, deuterated calibrants) has the potential to be adapted for more anionic metabolites.

Potential Phosphorus Uptake Mechanisms in the Deep Sedimentary Biosphere

Our understanding of phosphorus (P) dynamics in the deep subseafloor environment remains limited. Here we investigate potential microbial P uptake mechanisms in oligotrophic marine sediments beneath the North Atlantic Gyre and their effects on the relative distribution of organic P compounds as a function of burial depth and changing redox conditions. We use metagenomic analyses to determine the presence of microbial functional genes pertaining to P uptake and metabolism, and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) to characterize and quantify P substrates. Phosphorus compounds or compound classes identified with 31P NMR include inorganic P compounds (orthophosphate, pyrophosphate, polyphosphate), phosphonates, orthophosphate monoesters (including inositol hexakisphosphate stereoisomers) and orthophosphate diesters (including DNA and phospholipid degradation products). Some of the genes identified include genes related to phosphate transport, phosphonate and polyphosphate metabolism, as well as phosphite uptake. Our findings suggest that the deep sedimentary biosphere may have adapted to take advantage of a wide array of P substrates and could play a role in the gradual breakdown of inositol and sugar phosphates, as well as reduced P compounds and polyphosphates.

Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism.

SummarySoybean oil is one of the most consumed vegetable oils worldwide. Genetic improvement of its concentration in seeds has been historically pursued due to its direct association with its market value. Engineering attempts aiming to increase soybean seed oil presented different degrees of success that varied with the genetic design and the specific variety considered. Understanding the embryo’s responses to the genetic modifications introduced, is a critical step to successful approaches. In this work, the metabolic and transcriptional responses to AtWRI1 and AtDGAT1 expression in soybean seeds were evaluated. AtWRI1 is a master regulator of fatty acid (FA) biosynthesis, and AtDGAT1 encodes an enzyme catalysing the final and rate‐limiting step of triacylglycerides biosynthesis. The events expressing these genes in the embryo did not show an increase in total FA content, but they responded with changes in the oil and carbohydrate composition. Transcriptomic studies revealed a down‐regulation of genes putatively encoding for oil body packaging proteins, and a strong induction of genes annotated as lipases and FA biosynthesis inhibitors. Novel putative AtWRI1 targets, presenting an AW‐box in the upstream region of the genes, were identified by comparison with an event that harbours only AtWRI1. Lastly, targeted metabolomics analysis showed that carbon from sugar phosphates could be used for FA competing pathways, such as starch and cell wall polysaccharides, contributing to the restriction in oil accumulation. These results allowed the identification of key cellular processes that need to be considered to break the embryo’s natural restriction to uncontrolled seed lipid increase.

Ultrasensitive Determination of Sugar Phosphates in Trace Samples by Stable Isotope Chemical Labeling Combined with RPLC-MS.

Sugar phosphates are important metabolic intermediates in organisms and play a vital role in energy and central carbon metabolism. Profiling of sugar phosphates is of great significance but full of challenges due to their high structural similarity and low sensitivities in liquid chromatography (LC)-mass spectrometry (MS). In this study, we developed a novel stable isotope chemical labeling combined with the reversed-phase (RP)LC-MS method for ultrasensitive determination of sugar phosphates at the single-cell level. By chemical derivatization with 2-(diazo-methyl)-N-methyl-N-phenyl-benzamide (2-DMBA) and d5-2-DMBA, sugar phosphate isomers can obtain better separation and identification, and the detection sensitivities of sugar phosphates increased by 3.5-147 folds. The obtained limits of detection of sugar phosphates ranged from 5 to 16 pg/mL. Using this method, we achieved ultrasensitive and accurate quantification of 12 sugar phosphates in different trace biological samples. Benefiting from the improved separation and detection sensitivity, we successfully quantified five sugar phosphates (d-glucose 1-phosphate, d-mannose 6-phosphate, d-fructose 6-phosphate, d-glucose 6-phosphate, and seduheptulose 7-phosphate) in a single protoplast of Arabidopsis thaliana.

Structural Determinants of Sugar Alcohol Biosynthesis in Plants: The Crystal Structures of Mannose-6-Phosphate and Aldose-6-Phosphate Reductases.

Sugar alcohols are major photosynthetic products in plant species from the Apiaceae and Plantaginaceae families. Mannose-6-phosphate reductase (Man6PRase) and aldose-6-phosphate reductase (Ald6PRase) are key enzymes for synthesizing mannitol and glucitol in celery (Apium graveolens) and peach (Prunus persica), respectively. In this work, we report the first crystal structures of dimeric plant aldo/keto reductases (AKRs), celery Man6PRase (solved in the presence of mannonic acid and NADP+) and peach Ald6PRase (obtained in the apo form). Both structures displayed the typical TIM barrel folding commonly observed in proteins from the AKR superfamily. Analysis of the Man6PRase holo form showed that residues putatively involved in the catalytic mechanism are located close to the nicotinamide ring of NADP+, where the hydride transfer to the sugar phosphate should take place. Additionally, we found that Lys48 is important for the binding of the sugar phosphate. Interestingly, the Man6PRase K48A mutant had a lower catalytic efficiency with mannose-6-phosphate but a higher catalytic efficiency with mannose than the wild type. Overall, our work sheds light on the structure-function relationships of important enzymes to synthesize sugar alcohols in plants.

Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB

Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.

The Structure-Derived Mechanism of Box H/ACA Pseudouridine Synthase Offers a Plausible Paradigm for Programmable RNA Editing

The uridine to pseudouridine transformation, one of the most abundant and essential post-transcriptional modification of RNAs, is carried out by pseudouridine synthases (PSUs). Aside from a few very specific targets, pseudouridylation is performed by a ribonucleo-protein complex, box H/ACA PSU, containing four different proteins and a guide RNA. Mutations of PSUs cause serious diseases including dyskeratosis congenita (DC), various types of cancers, and nephrotic syndrome. Here, we combined homology modeling, classical force-field-based molecular dynamics, and quantum mechanics/molecular mechanics-based enhanced sampling free energy simulations to show that reactant destabilization through the severe distortion of the target uridine in the active site of box H/ACA PSU is a key factor in the catalysis of pseudouridylation. We propose a dissociation-rebound mechanism where the uracil detaches from the ribose by the cleavage of the C1′–N1 bond leading to a charge separated intermediate. The base rebounds to the ribose with its C5 carbon with a very small barrier. The subsequent tautomerization step is proposed to be coupled to the tilting of the upper dyskerin region, comprising the thumb loop, and product release. The proposed mechanism does not impose sequence restriction on the substrate; it only requires a complementary guide RNA coordinated to the protein components of the enzyme complex. We also found that the interactions of the guide RNA with the proteins of the complex in the vicinity of the active site are overwhelmingly formed by the sugar–phosphate backbone, indicating that designed guide RNAs could be applied to carry out pseudouridylation of substrates with a great variety of different sequence motifs. Therefore, the endogenous box H/ACA PSU system may be used to target premature stop codons, for example, to induce their read through serving as a vehicle for RNA editing and therapeutics for gene lesion-related diseases.

31P solid-state NMR on skeletal muscle of wild and farmed Atlantic salmon

Over the past 50 years, 31P NMR has proven a powerful tool for obtaining information on cellular biochemistry. Here we use this technique for the first time to study intracellular phosphorous metabolites in skeletal muscle tissue of wild and farmed salmon, to investigate possible effects due to differences in diet and way of life. The wild salmon sample shows a significantly more diverse composition of metabolites compared to the farmed salmon sample. The differences are evident in the entire spectrum, including regions displaying resonances from phosphomonoesters and sugar phosphates, as well as other molecules important for phospholipid metabolism.It is demonstrated that 31P MAS NMR can be used to study a broad range of phosphorus metabolites ex vivo, which can give useful information, both on its own or as a supplement to other extraction-based analyses. Further 31P MAS NMR investigations on farmed salmon raised under different controlled conditions may give important insights into the broad array of health issues seen in farmed salmon.

Exploration of phytate-mineralizing bacteria with multifarious plant growth-promoting traits.

Phytate-mineralizing bacteria (PMB) with plant growth-promoting activity can be considered as a potential biofertilizer for plant nutrition. PMB catalyzes the conversion of insoluble sugar phosphates, inositols, nucleic acids, phospholipids, nucleotides, phytate, and phytin into soluble forms that can be assimilated by plants. The present study aimed to isolate potential PMB from rhizospheric soils and to study their plant growth-promoting potential for the possible development of a potential phosphobacterium biofertilizer. For this purpose, 34 PMB isolates were isolated that showed potent phytate-mineralizing potential. These isolates were tested for their potential to solubilize tricalcium phosphate (TCP) and for various other plant growth-promoting activities. Significant differences were found among the isolates with regard to phytate mineralization and other plant growth-promoting characteristics. The bacterial isolates biochemically identified as Bacillus, Paenibacillus, Arthrobacter, and Burkholderia exhibited high/medium P solubilization, medium/high phytohormone production, and medium/low siderophore and ammonia production. Among all these isolates, isolate A14 (Burkholderia cenocepacia strain FDAARGOS_7) was the promising isolate with high TCP solubilization, medium phytate mineralization, high enzyme production, medium/high phytohormone production, and medium ammonia production. This strain also showed nitrogen fixation activity, zinc solubilizing potential, potassium solubilization, ACC deaminase production, and catalase production. Hence, it can be concluded that B. cenocepacia can be the potential candidate for biofertilizer development. Future studies are planned for exploring the role of PMB in biofertilizer formulations.

The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos

The CO2-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IAC clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.

GTP binding to translation factor eIF2B stimulates its guanine nucleotide exchange activity

SummaryeIF2B is the guanine nucleotide exchange factor (GEF) required for cytoplasmic protein synthesis initiation in eukaryotes and its regulation within the integrated stress response (ISR). It activates its partner factor eIF2, thereby promoting translation initiation. Here we provide evidence through biochemical and genetic approaches that eIF2B can bind directly to GTP and this can enhance its rate of GEF activity toward eIF2–GDP in vitro. GTP binds to a subcomplex of the eIF2Bγ and ε subunits. The eIF2Bγ amino-terminal domain shares structural homology with hexose sugar phosphate pyrophosphorylase enzymes that bind specific nucleotides. A K66R mutation in eIF2Bγ is especially sensitive to guanine or GTP in a range of functional assays. Taken together, our data suggest eIF2Bγ may act as a sensor of purine nucleotide availability and thus modulate eIF2B activity and protein synthesis in response to fluctuations in cellular nucleotide levels.

Coupling Mixed Mode Chromatography/ESI Negative MS Detection with Message-Passing Neural Network Modeling for Enhanced Metabolome Coverage and Structural Identification.

A key unmet need in metabolomics continues to be the specific, selective, accurate detection of traditionally difficult to retain molecules including simple sugars, sugar phosphates, carboxylic acids, and related amino acids. Designed to retain the metabolites of central carbon metabolism, this Mixed Mode (MM) chromatography applies varied pH, salt concentration and organic content to a positively charged quaternary amine polyvinyl alcohol stationary phase. This MM method is capable of separating glucose from fructose, and four hexose monophosphates a single chromatographic run. Coupled to a QExactive Orbitrap Mass Spectrometer with negative ESI, linearity, LLOD, %CV, and mass accuracy were assessed using 33 metabolite standards. The standards were linear on average >3 orders of magnitude (R2 > 0.98 for 30/33) with LLOD < 1 pmole (26/33), median CV of 12% over two weeks, and median mass accuracy of 0.49 ppm. To assess the breadth of metabolome coverage and better define the structural elements dictating elution, we injected 607 unique metabolites and determined that 398 are well retained. We then split the dataset of 398 documented RTs into training and test sets and trained a message-passing neural network (MPNN) to predict RT from a featurized heavy atom connectivity graph. Unlike traditional QSAR methods that utilize hand-crafted descriptors or pre-defined structural keys, the MPNN aggregates atomic features across the molecular graph and learns to identify molecular subgraphs that are correlated with variations in RTs. For sugars, sugar phosphates, carboxylic acids, and isomers, the model achieves a predictive RT error of <2 min on 91%, 50%, 77%, and 72% of held-out compounds from these subsets, with overall root mean square errors of 0.11, 0.34, 0.18, and 0.53 min, respectively. The model was then applied to rank order metabolite IDs for molecular features altered by GLS2 knockout in mouse primary hepatocytes.

Using biochar to strengthen the removal of antibiotic resistance genes: Performance and mechanism

In this study, the excess activated sludge was used for pyrolysis to produce biochar with Ce modification. The removal process and mechanism of ampicillin resistance gene (ARGAmp) by biochar was investigated. The results showed that when pyrolyzing the excess sludge at 400 °C, the organic components in the sludge could be partially pyrolyzed and complexed with Ce. By accepting electrons from phenol or quinone, persistent free radicals (PFRs) were formed on the surface of biochar. On the optimized conditions with the initial ARGAmp concentration of 41.43 mg/L, the removal ratios of ARGAmp by adsorption, PFRs, hydroxyl free radicals (·OH) by adding H2O2 were 28.37%, 8.26%, and 27.56%. No melted DNA was detected in the treated samples. The oxidation process by PFRs and ·OH can directly destroy the ARGAmp structure. The phosphodiester bond in the base stacking structure and the phosphate bond in the nucleotide are the possible action sites of PFRs. Treated ARGAmp products were in the form of base pair residues or short-chain double helix structures. ·OH can be added to the bases of nucleotide molecules to form highly active free radical adducts. They can initiate molecular dehydrogenation and intermolecular proton transfer, resulting in oxidation of the base to the scission of the phosphate sugar backbone.

Edukasi Pengaruh pH Media dan Lama Fermentasi Terhadap Basil Nata de Coco

Nata is one of the organic food products that has a high fiber content. Nata is a product of fermentation by Acetobacter xylinum. The review that discusses the making of nata by analyzing the effect of the pH of the media and the duration of fermentation at the same time is still very limited. Thus, this review aims to discuss the effect of media pH and fermentation time on nata de coco bacilli. Paying attention to the factors that affect the growth of Acetobacter xylinum bacteria during the fermentation process needs to be done so that it can produce nata de coco with optimum thickness and weight and a chewy texture. These factors include the pH of the media and the length of fermentation. The ingredients for making nata de coco consist of coconut water, granulated sugar, ZA or Ammonium phosphate, and Acetobacter xylinum seeds. The method of implementing the activity which consists of counseling and practice of making nata de coco is able to increase the knowledge of residents, teachers, students (i) about nata de coco and coconut water which are potential natural plants (natural products), as well as skills (soft skills) in making nata de coco. The teachers, students(i) and residents admitted that they were greatly helped by this activity as a form of training that could be applied in their daily lives in entrepreneurship, even though it was a small scale.Keyword: nata de coco, media pH, fermentation time, education

Phosphorus retention within a relic agricultural ditch in a constructed wetland.

Stormwater treatment areas (STAs) are constructed wetlands established to capture phosphorus (P) from agricultural runoff before reaching the Florida Everglades. Retained P is primarily stored in wetland soils and sediments generated through a collection of interrelated physical, chemical, and biological processes. The amount of P and other elements (Al, Ca, Cu, Fe, Mg, Mn, Pb, and Zn) retained in the flocculent (floc) and recently accreted soil (RAS) horizons from a relic agricultural ditch within Cell 4S of STA-1E were compared with the surrounding marsh soils (upstream and downstream sites of the ditch). The amount of P retained in the ditch was significantly greater than the surrounding marsh soils and for all the elements in the floc horizon and five of the nine elements in the RAS horizon, suggesting that different processes or process rates influenced accumulation. Phosphorus species in the floc and RAS sediment horizons were identified and quantified using 31 P nuclear magnetic resonance (NMR) spectroscopy and total P determined by microwave plasma-optical emission spectroscopy. In general, P forms were dominated by orthophosphate, sugar phosphates, nucleotides, DNA, and pyrophosphate, with varying relative abundances of species. Total P concentration significantly decreased from upstream to downstream of the ditch by an average of 28 and 35% for floc and RAS soils, respectively. The relatively high P accrual rate within the ditch suggested that relic ditches perpendicular to flow could reduce P transport to downstream soils and sediments and, in turn, help maintain low P levels in overlying water.

Fast filtration with a vacuum manifold system as a rapid and robust metabolome sampling method for Saccharomyces cerevisiae

For metabolome sample preparation, rapid quenching of cellular metabolism without severe loss of intracellular metabolites is important. Here, we comparatively evaluated the two sampling methods, cold methanol quenching and fast filtration, for one of the most important industrial microorganisms, yeast Saccharomyces cerevisiae. The latter, using a vacuum manifold system capable of processing up to twenty samples simultaneously, was developed here. The results showed that the cold methanol quenching method resulted in severe losses of intracellular metabolites but that sugars and sugar phosphates were highly preserved. In comparison, the fast filtration method better preserved most metabolites with less extracellular contamination. Our results suggested that the fast filtration method with a vacuum manifold system can be widely applied to yeast metabolome analysis due to its simplicity, robustness, and lack of significant intracellular metabolite loss.

Dictyoglomus turgidum DSM 6724 α-Glucan Phosphorylase: Characterization and Its Application in Multi-enzyme Cascade Reaction for D-Tagatose Production.

Phosphorylase is a type of enzyme-producing sugar phosphates through the reversible phosphorolysis reactions of glycosides, which makes it an important starting enzyme in multi-enzyme systems for rare sugar biomanufacturing. To investigate its application in D-tagatose biosynthesis from maltodextrin using in vitro multi-enzyme cascade biosystem, the α-glucan phosphorylase (αGP; EC 2.4.1.1) from the thermophile D. turgidum DSM 6724 was prepared and characterized. It exhibited the specific activity of 30.28 U/mg at its optimal temperature of 70°C. Thermostability results revealed that DituαGP could maintain more than 25% of initial activity for 4h, even at 90°C. The highest activity was observed at pH 5.5, and most divalent metal ions deactivated the enzyme. DituαGP exhibited great application potential in the multi-enzyme system that about 3.919g/L of D-tagatose was produced from 150g/L of maltodextrin within 36h. DituαGP has played an important role in this biosystem and will also be applied in the synthesis of other rare sugars from maltodextrin.

减库对大豆叶片碳代谢的影响

<p id="C3">Carbon metabolism is one of the most obvious physiological processes affected by source-sink relationship, which is closely related to plant growth and yield formation. The study of the effect of sink-limiting treatment on carbon metabolism of soybean leaf can provide a theoretical basis for understanding yield reduction mechanism caused by the imbalance of source-sink relationship. Taking early maturing soybean Sudou 13 as materials, pool experiments were carried out at the soybean experimental station of Jiangsu Academy of Agricultural Sciences in 2019 and 2020. The sink-limiting treatments (all pods removal, 1/2 pods removal, and all seed injury) were conducted at R4 stage, and intact (fully podded) plants were used as control. The results showed that sink-limiting treatments delayed leaf senescence and abscission and caused stay-green. Sink-limiting treatments inhibited the net photosynthetic rate (<italic>P</italic>_n) in a short time after treatment, but did not affect the initial carboxylation rate (ɑ), and the decrease of <italic>P</italic>_n was mainly restricted by stomata limitation. With the prolongation of the time after treatment, the inhibition effect on photosynthesis gradually weakened and turned into a promoting effect. At late growth stages, the stay-green syndrome leaves still maintain relatively higher initial carboxylation rate (<italic>a</italic>), sugar phosphate synthase (SPS), sucrose synthase (SuSy), acid invertase (SAI) activity, photosynthetic pigment, soluble sugar, starch, sucrose, and fructose content, which was beneficial to maintaining a relatively high photosynthetic performance. Sink-limiting treatments induced more photosynthetic products to be distributed to vegetative organs, and stimulated stems and leaves to be new sink organs in certain extent, which was beneficial to the output of photosynthetic products and maintained relatively high levels of carbon metabolism of leaves at late growth stages. The effects of removing all pods and seed injury treatments on delaying leaf senescence and abscission, reducing photosynthetic performance and carbon metabolism was significantly higher than those of removing 1/2 pod. In conclusion, sink-limiting under the same source condition could induce stay-green syndrome. The greater the degree of sink-limiting, the more severe the green retention. Sink-limiting treatment significantly affected the carbon metabolism of soybean plant, although it inhibited photosynthetic performance in a short period after treatment. It maintained higher photosynthetic and key enzyme activities of carbon metabolism at late growth stages, which was conducive to the synthesis of more carbohydrates and stimulated the stems, leaves, and petioles to transform into new sink organs to a certain extent.

DNA Dynamics under Periodic Force Effects.

The sensitivity of DNA to electromagnetic radiation in different ranges differs depending on various factors. The aim of this study was to examine the molecular dynamics of DNA under the influence of external periodic influences with different frequencies. In the present paper, within the framework of a mechanical model without simplifications, we investigated the effect of various frequencies of external periodic action in the range from 1011 s−1 to 108 s−1 on the dynamics of a DNA molecule. It was shown that under the influence of an external periodic force, a DNA molecule can perform oscillatory movements with a specific frequency characteristic of this molecule, which differs from the frequency of the external influence ω. It was found that the frequency of such specific vibrations of a DNA molecule depends on the sequence of nucleotides. Using the developed mathematical model describing the rotational motion of the nitrogenous bases around the sugar–phosphate chain, it is possible to calculate the frequency and amplitude of the oscillations of an individual DNA area. Such calculations can find application in the field of molecular nanotechnology.

Inactivation of viruses using nonthermal plasma in viral suspensions and foodstuff: A short review of recent studies

AbstractThis review tries to introduce the novel and promising technology of the nonthermal plasma against different viruses and virus surrogates, which can trigger food infections and gastroenteritis. It has been reported that the noroviruses are responsible for 21 million cases of gastrointestinal illness annually just in the United States. The article is divided into the introduction for nonthermal plasma, its antiviral mechanism, and the most effective parameters on its antiviral functionality. This technology offers many advantages, including simple in designing, leaving no toxic residues, fast processing, and no thermal degradation of samples. According to the accomplished studies, the exposure distance, processing time, and generated amount of reactive species, particularly singlet oxygen are the main parameters affecting the performance of nonthermal plasma against food viruses. Especially, the capsid and genome of viruses seem to be under influence of nonthermal plasma. Deformation of the capsid envelope through oxidation and damage to the sugar phosphate backbone of viral RNA and DNA are considered the most important factors of reactive species generated by nonthermal plasma on viruses.