Phylogenetic classification of Pseudomonas putida strains by MALDI-MS using ribosomal subunit proteins as biomarkers

A new method for phylogenetic classification of bacterial strains using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is proposed. This method was developed using a bioinformatics-based approach to the rapid identification of bacteria as previously proposed by Demirev and co-workers, which uses ribosomal proteins composed of approximately 50 subunit proteins as biomarkers. Although the amino acid sequences of ribosomal proteins are highly conserved, slight sequence variations can occur at the strain level. Since ribosomal subunit proteins are a complex of housekeeping proteins that have different phylogenetic evolution rates, sequence variation detected as mass differences by MALDI-MS may be useful for the phylogenetic classification of bacteria at strain level. In our proposed method, the first step is the selection of reliable biomarkers through characterization of the expressed ribosomal subunit proteins of a reference strain (usually a genome-sequenced strain) by MALDI-MS. The observed masses in the MALDI mass spectra of cell lysates of sample strains are then compared with the biomarker masses of the reference strain. The biomarkers for each sample strain were designated as present or absent at the reference masses, indicated by 1 or 0, respectively, which were summarized in a table. This table is processed by cluster analysis, generating a phylogenetic tree. In this study, the success of this approach was confirmed by classification of Pseudomonas putida strains because its classification is much more complicated than that of other bacterial strains. Forty-three reliable biomarkers were selected from ribosomal sub-unit proteins of a genome-sequenced strain, P. putida KT2440. The numbers and kinds of biomarkers observed for 16 strains of P. putida, including different biovars, were markedly different, reflecting the variety of the strains. The classification results by the proposed method were highly comparable to those based on the DNA gyrase subunit B gene (gyrB) sequence analysis, suggesting our proposed method would be a useful high-throughput method for phylogenetic classification of newly isolated bacteria.     

Vascular bundle shape in cross-section and relaxation properties of Moso bamboo (Phyllostachys pubescens)

The variation in the longitudinal and radial direction of the R/T ratio which is the ratio of the radially maximum length (R) to the tangentially maximum width (T) of a vascular bundle and area ratio of vascular bundles, which are cross-sectional image features of bamboo, and the relationships between the R/T ratio or area ratio and relaxation behavior were investigated. These image features varied characteristically in the longitudinal and radial directions. Relationships between these image features and relaxation behavior were evaluated using the instantaneous creep compliance ln[J (0)] and the creep intensity ln [J(3 × 10⁴) ? J (0)]. Although both instantaneous compliance and creep intensity decreased as density increased, their dependence properties were remarkably different. Instantaneous compliance was strongly correlated with R/T ratio and density, which was related to the area ratio, whereas creep intensity was weakly correlated with density in a given range. The results indicate a difference between the two relaxation properties, because creep intensity depends more on microstructures, such as the conformation of molecular chains in the substance, or interactions among cells than on R/T ratio and area ratio image features.     

CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands

Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (VEGF, C-KIT, BCL2, and HRAS). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands.     

Surface-Diluted LiMn6 Superstructure Units Utilizing PO43− Confined Ni-Doping Sites to Stabilize Li-Rich Layered Oxides

Serious capacity and voltage degradation of Li-rich layered oxides (LLOs) caused by severe interfacial side reactions (ISR), structural instability, and transition metal (TM) dissolution during charge/discharge need to be urgently resolved. Here, it is proposed for the inaugural time that the confinement effect of PO₄³⁻ dilutes the LiMn₆ superstructure units on the surface of LLOs, while deriving a stable interface with phosphate compounds and spinel species. Combining theoretical calculations, diffraction, spectroscopy, and micrography, an in-depth investigation of the mechanism is performed. The results show that the modified LLO exhibits excellent anionic/cationic redox reversibility and ultra-high cycling stability. The capacity retention is increased from 72.4% to 95.4%, and the voltage decay is suppressed from 2.48 to 1.29 mV cycle⁻¹ after 300 cycles at 1 C. It also has stable long cycling performance, with capacity retention improved from 40.2% to 81.9% after 500 cycles at 2 C. The excellent electrochemical performance is attributed to the diluted superstructure units on the surface of LLO inhibiting the TM migration in the intralayer and interlayer. Moreover, the stable interfacial layers alleviate the occurrence of ISR and TM dissolution. Therefore, this strategy can give some important insights into the development of highly stable LLOs.     

Characterization and Pharmacokinetic Profile of Herbs and Spices' Phytochemicals over 24 h after Consumption in Overweight/Obese Adults

Scope

This study aims to characterize the phytochemicals in commonly consumed herbs/spices (H/S) in the United States and their pharmacokinetic profile (PK) over 24 h in humans after consumption.

Method and results

The clinical trial is a randomized, single-blinded, four-arm, 24 h, multi-sampling, single-center crossover design (Clincaltrials.gov NCT03926442) conducted in obese/overweight adults (n = 24, aged 37 ± 3 years, BMI = 28.4 ± 0.6 kg m⁻²). Study subjects consume a high-fat high-carbohydrate meal with salt and pepper (control) or the control meal with 6 g of three different H/S mixtures (Italian herb: rosemary, basil, thyme, oregano, and parsley in the same ratio; cinnamon; and pumpkin pie spice containing cinnamon, ginger, nutmeg, and allspice, the ratio is unknown). Three H/S mixtures are analyzed and 79 phytochemicals are tentatively identified and quantified. Following H/S consumption, 47 metabolites are tentatively identified and quantified in plasma samples. The PK data suggest that some metabolites appear in blood as early as 0.5 h while others can extend up to 24 h.

Conclusion

Phytochemicals from H/S include in a meal are absorbed and undergo phase I and phase II metabolism and/or catabolized to phenolic acids peaking at different times.