Interaction between Heavy Water and Single-Strand DNA: A SERS Study

The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental D2O. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between D2O and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing D2O proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and D2O and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and D2O. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules

ZIF-67 grown onto three-dimensional biomass cotton fibers for efficient adsorption of tetracycline

In recent years, Metal-Organic Frameworks (MOFs) have garnered significant attention for their potential in tetracycline (TC) removal. However, pure MOFs typically exist in powdered form and tend to aggregate in water, which greatly limits practical applications. To address this issue, a three-dimensional composite material was prepared by ZIF-67 grown onto cotton fibers (ZIF-670.50@CF). This composite not only enhances adsorption capacity but also reduces the adsorption equilibrium time compared to most other adsorbents. ZIF-670.50@CF boasts a BET specific surface area of 257.74 m²·g-1, with pores consisting mainly of mesopores and micropores. Moreover, ZIF-670.50@CF exhibits excellent adsorption capabilities for TC across a broad pH range of 4–9 and displays notable resilience against environmental interference. The adsorption behavior of ZIF-670.50@CF is more consistent with the Langmuir model, with a maximum adsorption capacity of 432.619 mg·g-1 for TC. Mechanistic research reveals that adsorption primarily involves chemical interactions (complexation, π-π stacking, and electrostatic interaction) and physical pore filling. Additionally, the favorable plasticity of ZIF-670.50@CF allows it to be fabricated into various shapes for use as filling materials, exhibiting admirable TC removal performance in continuous flow adsorption experiments

Experimental Investigation on Oil Enhancement Mechanism of Hot Water Injection in tight reservoirs

Aimed at enhancing the oil recovery of tight reservoirs, the mechanism of hot water flooding was studied in this paper. Experiments were conducted to investigate the influence of hot water injection on oil properties, and the interaction between rock and fluid, petrophysical property of the reservoirs. Results show that with the injected water temperature increasing, the oil/water viscosity ratio falls slightly in a tight reservoir which has little effect on oil recovery. Further it shows that the volume factor of oil increases significantly which can increase the formation energy and thus raise the formation pressure. At the same time, oil/water interfacial tension decreases slightly which has a positive effect on production though the reduction is not obvious. Meanwhile, the irreducible water saturation and the residual oil saturation are both reduced, the common percolation area of two phases is widened and the general shape of the curve improves. The threshold pressure gradient that crude oil starts to flow also decreases. It relates the power function to the temperature, which means it will be easier for oil production and water injection. Further the pore characteristics of reservoir rocks improves which leads to better water displacement. Based on the experimental results and influence of temperature on different aspects of hot water injection, the flow velocity expression of two-phase of oil and water after hot water injection in tight reservoirs is obtained

Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy

Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures

Bacterial Diversity and Lactic Acid Bacteria with High Alcohol Tolerance in the Fermented Grains of Soy Sauce Aroma Type Baijiu in North China

Soy sauce aroma type baijiu (also known as Maotai-flavor baijiu) is one of the most popular types of baijiu in China. Traditionally, it is mainly produced in Southwest China. However, in recent decades, some other regions in China have also been able to produce high-quality soy sauce aroma type baijiu, but their microbial flora characteristics during fermentation are still unclear. Here, the bacterial microbial community structure of fermented grains in different rounds of Lutaichun soy sauce aroma type baijiu produced in North China was studied by high-throughput sequencing technology, and the potential probiotics strains with good characteristics (alcohol tolerance, etc.) were screened. The results showed that lactic acid bacteria were the main bacteria in the process of baijiu fermentation. However, as the number of repeated fermentation rounds increased, the proportion of lactic acid bacteria decreased. Firmicutes (96.81%) were the main bacteria in baijiu fermentation at the phylum level, and Lactobacillus (66.50%) were the main bacteria at the genus level. Finally, two strains with high resistance to alcohol stress, Lactiplantibacillus plantarum LTJ12 and Pediococcus acidilactici LTJ28, were screened from 48 strains of lactic acid bacteria in the fermented grains. The survival rates of L. plantarum LTJ12 and P. acidilactici LTJ28 under the 8% alcohol stress treatment were 59.01% and 55.50%, respectively. To the best of our knowledge, this study is the first to reveal the microbial succession of fermented grains in different rounds of soy sauce aroma type baijiu from North China, and has the benefit of explaining the deep molecular mechanism in the process of baijiu fermentation. In addition, the obtained lactic acid bacteria strains with high alcohol tolerance could be conducive to the development of new products such as active probiotic alcoholic beverages and may have important industrial development prospects also

Comparative Genomics Analysis Provides New Insights into High Ethanol Tolerance of <i>Lactiplantibacillus pentosus</i> LTJ12, a Novel Strain Isolated from Chinese Baijiu

Lactic acid bacteria have received a significant amount of attention due to their probiotic characteristics. The species Lactiplantibacillus plantarum and Lactiplantibacillus pentosus are genotypically closely related, and their phenotypes are so similar that they are easily confused and mistaken. In the previous study, an ethanol-resistant strain, LTJ12, isolated from the fermented grains of soy sauce aroma type baijiu in North China, was originally identified as L. plantarum through a 16S rRNA sequence analysis. Here, the genome of strain LTJ12 was further sequenced using PacBio and Illumina sequencing technology to obtain a better understanding of the metabolic pathway underlying its resistance to ethanol stress. The results showed that the genome of strain LTJ12 was composed of one circular chromosome and three circular plasmids. The genome size is 3,512,307 bp with a GC content of 46.37%, and the number of predicted coding genes is 3248. Moreover, by comparing the coding genes with the GO (Gene Ontology), COG (Cluster of Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, the functional annotation of the genome and an assessment of the metabolic pathways were performed, with the results showing that strain LTJ12 has multiple genes that may be related to alcohol metabolism and probiotic-related genes. Antibiotic resistance gene analysis showed that there were few potential safety hazards. Further, after conducting the comparative genomics analysis, it was found that strain LTJ12 is L. pentosus but not L. plantarum, but it has more functional genes than other L. pentosus strains that are mainly related to carbohydrate transport and metabolism, transcription, replication, recombination and repair, signal transduction mechanisms, defense mechanisms and cell wall/membrane/envelope biogenesis. These unique functional genes, such as gene 2754 (encodes alcohol dehydrogenase), gene 3093 (encodes gamma-D-glutamyl-meso-diaminopimelate peptidase) and some others may enhance the ethanol tolerance and alcohol metabolism of the strain. Taken together, L. pentosus LTJ12 might be a potentially safe probiotic with a high ethanol tolerance and alcohol metabolism. The findings of this study will also shed light on the accurate identification and rational application of the Lactiplantibacillus species

Anchor carbon dots inside NH2-MIL-88B via ship-in-a-bottle strategy for dual signal enhancement in colorimetric-fluorescent sensors

The increase in oxytetracycline (OTC) pollution has become a significant risk to ecological stability and human health because of excessive use. Therefore, developing a precise and reliable sensor for trace OTC detection is critical. In this work, a dual-mode sensor of colorimetric-fluorescent (CL-FL) with dual signal-on was developed for OTC detection. Firstly, a novel carbon dots encapsulating in cavities of MOFs composite (CDs@NH2-MIL-88B) was constructed by the ship-in-a-bottle approach, which enhanced peroxidase-like activity and fluorescent intensity. Further, combining with surface molecularly imprinted polymer (MIP), the dual-mode sensor was constructed to develop selectivity (CDs@NH2-MIL-88B@rMIP). Finally, the dual signal enhancement mechanism of the sensor comes from the interaction between OTC and identifying binding site involving strong hydrogen bonding and metal complexation from imprinted cavity and CDs@NH2-MIL-88B, respectively. The prepared sensor has a linear detection range of 1.00 × 10−9 - 1.00 × 10−5 M with the limit of detection (LOD) of 1.47 × 10−10 M for the CL mode and a detection range of 1.00 × 10−11 −1.00 × 10−7 M with the LOD of 1.84 × 10−12 M for the FL mode. Meanwhile, the sensor shows high sensitivity, accuracy and reliability in OTC detection. Overall, this work provides a promising CL-FL dual-mode sensing systems with signal-on in the detection of antibiotics and other hazardous pollutants