Electronic characteristics of BRCA1 mutations in DNA.

The efficient and low-cost way for gene mutation detection and identification are conducive for the detection of disease. Here, we report the electronic characteristics of the gene of breast cancer 1 in four common mutation types: duplication, single nucleotide variant, deletion, and indel. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. The magnitude of conductance of these DNA molecules and mutational changes are found to be detectable experimentally. In this study, we also find the significant mutation type dependent on the change of conductance. Hence these mutations are expected to be identifiable. We find deletion type mutation shows the largest change in relative conductance (~97%), whereas the indel mutation shows the smallest change in relative conductance (~27%). Therefore, this work presents a possibility of electronic detection and identification of mutations in DNA, which could be an efficient method as compared to the conventional methods.

Effect of cytosine hydroxymethylation on DNA charge transport.

DNA hydroxymethylation plays a very important role in some biological processes, such as DNA methylation process. In addition, its presence can also cause some diseases. In this paper, the electrical properties of cytosine hydroxymethylated (Chm) DNA sequences are studied. The density functional theory (DFT) and Landauer-Büttiker framework are used to study the decoherence conductance and transmission of the Chm strands in different configurations, which provides a theoretical basis for the detection of Chm. The results show that the conductance of the hydroxymethylated DNA strand is smaller than that of the native and methylated strands. The length dependence of the Chm strands is also studied. With the length increasing, the conductance becomes larger. This study shows that DNA methylation can be detected electrically.

Analysis of differential expression proteins reveals the key pathway in response to heat stress in Alicyclobacillus acidoterrestris DSM 3922T.

For the purpose of investigating the heat resistance mechanism of Alicyclobacillus acidoterrestris, label-free quantification was used to reveal some cellular changes in A. acidoterrestris during heat stress. Totally, 545 differential expression proteins were respectively identified at heat stress of 65 °C for 5 min, of which 258 proteins were up-regulated and 287 proteins were down-regulated. These significantly changed proteins were mapped to 100 pathways and some of them were mostly related to protection or repair of macromolecules such as proteins and DNA, cell wall formation, which indicated that these proteins might play crucial roles in response to heat stress. The KEGG pathway analysis combined with protein functional analysis and further validation at mRNA level suggested that A. acidoterrestris sensed the temperature rise in environment through alterations in the secondary structure of DNA and RNA molecules. The biosynthesis of antibiotics pathway and the ribosomes might be involved in signal transduction in heat stress and further trigger a large number of proteins playing a critical role in the regulation of heat stress in A. acidoterrestris. The study firstly demonstrated the global physiological response to heat stress and the results provided a better understanding of thermal adaption mechanism of A. acidoterrestris.

Enhancing the formation of functional glucosinolate degradation products in fermented broccoli stalk by-product with lactic acid bacteria.

Broccoli stalk by-product (BsBP) is rich in glucosinolates (GSLs). Its fermentation process is generally characterized by the degradation of GSLs and formation of bioactive isothiocyanates (ITCs), in which lactic acid bacteria (LAB) play an important role. The GSLs-degrading capacity of 61 LAB strains was investigated in vitro. Lacticaseibacillus paracasei YC5, Pediococcus pentosaceus RBHZ36, and Lactiplantibacillus plantarum ND1, with high potential to transform GSLs into ITCs, were screened. The functional GSL degradation products (total content of sulforaphane, indol-3-carbinol, and ascorbigen) increased 22.0-33.5 % compared to natural fermentation after 24 h when BsBP was fermented by the three screened strains in pure culture. LAB fermentation also helped to increase the quantity of indolic GSL degradation products in BsBP brine, suggesting that LAB fermentation promoted BsBP GSLs transformation into bioactive ITCs. The proposed use of the LAB strains characterized in this study provided a fermented BsBP and brine with high profile of functional GSL degradation products.

Interaction mechanism of okra (Abelmoschus esculentus L.) seed protein and flavonoids: Fluorescent and 3D-QSAR studies.

The binding capacity of 10 flavonoids with okra seed protein (OSP) was studied by fluorescence spectroscopy. The structure of flavonoids had an obvious impact on binding performance. The binding ability of flavanone was lower than that of flavone, isoflavone and dihydrochalcone. The binding capacity of flavonoid glycoside was superior to that of the corresponding flavonoid aglycone. The binding ability was positively correlated with the number of phenolic hydroxyl groups on the B ring. The steric field and electrostatic field model constructed by 3D-QSAR method could well explain the above interaction behavior. Thermodynamic analysis suggested that the quenching mechanism of OSP caused by flavonoids was static quenching, and the binding-site number was 1. In addition, hydrogen bonding and van der Waals force dominated this interaction. The 3D and synchronous fluorescence spectra showed that there was no significant change in the polarity of the environment around tryptophan and tyrosine residues during binding.

Variation in glucosinolates and the formation of functional degradation products in two Brassica species during spontaneous fermentation.

Vegetables from the Brassica species are excellent sources of glucosinolates (GLSs), the precursors of health-promoting isothiocyanates (ITCs). Fermentation enhances the biotransformation of GLSs into potential bioactive ITCs. To explore the biotransformation of GLSs during Brassica fermentation, the changes in GLSs during the fermentation of two Brassica species (i.e., cauliflower and broccoli); the formation of corresponding breakdown products; and the shifts in physicochemical parameters, bacterial communities, and myrosinase activities involved in GLSs degradation were systematically investigated. Nine aliphatic, three indolic, and two benzenic GLSs were identified in fermented cauliflower (FC) and fermented broccoli (FB). Aliphatic glucoiberin and glucoraphanin were the major forms of GLS in FC and FB, respectively; indolic glucobrassicin was also abundant in both FC and FB. The total GLS content decreased by 85.29% and 65.48% after 3 d of fermentation in FC and FB, respectively. After 2 d of fermentation, a significant increase in bioactive GLS degradation products (P < 0.05), including sulforaphane (SFN), iberin (IBN), 3,3-diindolylmethane (DIM), and ascorbigen (ARG), was observed in FC and FB compared to in fresh cauliflower and broccoli. Moreover, variations in pH value and titratable acidity in FC and FB correlated with Brassica fermentation and were accomplished by lactic acid bacteria, including Weissella, Lactobacillus-related genera, Leuconostoc, Lactococcus, and Streptococcus. These changes may enhance the biotransformation of GSLs to ITCs. Overall, our results indicate fermentation leads to the degradation of GLSs and the accumulation of functional degradation products in FC and FB.

Charge transport properties of SARS-CoV-2 Delta variant (B.1.617.2).

The B.1.617.2 (Delta) variant of concern is causing a new wave of infections in many countries. In order to better understand the changes of the SARS-CoV-2 mutation at the genetic level, we selected six mutations in the S region of the Delta variant compared with the native SARS-CoV-2 and get the conductance information of these six short RNA oligonucleotides groups by construct RNA: DNA hybrids. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. We found that conductance is very sensitive to small changes in virus sequence. Among the 6 mutations in the Delta S region, D950N shows the largest change in relative conductance, reaching a surprising 4104.75%. These results provide new insights into the Delta variant from the perspective of its electrical properties. This may be a new method to distinguish virus variation and possess great research prospects.

Preparation and characterization of a dihydromyricetin-sugar beet pectin covalent polymer.

A dihydromyricetin (DMY)-sugar beet pectin (SBP) covalent polymer was prepared using an alkaline method for the first time, and its structure and physicochemical properties were characterized. The results showed that the molecular weight, total phenol content, and ABTS radical scavenging ability of the polymer were positively correlated with DMY dosage. The polymer inhibited α-glucosidase in a mixed non-competitive and anti-competitive inhibition manner, and its inhibition performance depended on the total phenol content. Its maximum inhibitory activity was much higher than that of DMY, which was attributed to its strong protein binding capacity. The stability and ß-carotene protective effects of the nano-emulsions stabilized with the DMY-SBP polymers were also positively correlated to the total phenol content and were superior to those stabilized by SBP. Therefore, the results obtained in this study may improve our functional understanding of natural polyphenol-polysaccharide polymers and promote the development of new nutraceuticals.

Interaction Mechanism of Flavonoids and α-Glucosidase: Experimental and Molecular Modelling Studies.

Flavonoids are known to play a role in hypoglycemia by inhibiting α-glucosidase. However, their interaction mechanism with α-glucosidase still needs to be elaborated. In this study, the α-glucosidase inhibitory activities of 15 flavonoids were investigated. Their molecular volume had a negative effect on inhibitory activity, while the number of phenolic hydroxyl groups on the B ring was positively correlated with inhibitory activity. To explain the significant differences in activity, the interaction behaviors of myricetin and dihydromyricetin, which have similar structures, were compared by spectrofluorimetry, molecular docking, and the independent gradient model (IGM). In the fluorescence analysis, myricetin exhibited a higher binding capacity. Based on molecular docking and IGM analysis, their non-covalent interactions with α-glucosidase could be visualized and quantified. It was found that they had different binding modes with the enzymes and that myricetin possessed stronger hydrogen bonding and van der Waals force interactions, which explained the thermodynamic results.