Microscopic and spectroscopic analysis of atmospheric iron-containing single particles in Lhasa, Tibet.

The Tibetan Plateau, known as the "Third Pole", is currently in a state of perturbation caused by intensified human activity. In this study, 56 samples were obtained at the five sampling sites in typical area of Lhasa city and their physical and chemical properties were investigated by TEM/EDS, STXM, and NEXAFS spectroscopy. After careful examination of 3387 single particles, the results showed that Fe should be one of the most frequent metal elements. The Fe-containing single particles in irregular shape and micrometer size was about 7.8% and might be mainly from local sources. Meanwhile, the Fe was located on the subsurface of single particles and might be existed in the form of iron oxide. Interestingly, the core-shell structure of iron-containing particles were about 38.8% and might be present as single-, dual- or triple-core shell structure and multi-core shell structure with the Fe/Si ratios of 17.5, 10.5, 2.9 and 1.2, respectively. Meanwhile, iron and manganese were found to coexist with identical distributions in the single particles, which might induce a synergistic effect between iron and manganese in catalytic oxidation. Finally, the solid spherical structure of Fe-containing particles without an external layer were about 53.4%. The elements of Fe and Mn were co-existed, and might be presented as iron oxide-manganese oxide-silica composite. Moreover, the ferrous and ferric forms of iron might be co-existed. Such information can be valuable in expanding our understanding of Fe-containing particles in the Tibetan Plateau atmosphere.

Nocardioides guangzhouensis sp. nov., an actinobacterium isolated from soil.

A Gram-positive, aerobic, non-spore-forming, non-pigmented and non-motile actinobacterial strain was isolated from a soil sample collected in Guangzhou, China. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 130T is most closely related to the type strain Nocardioides iriomotensis NBRC 105384T, with a sequence similarity of 97.69 %. The isolate was distinguished from this phylogenetically related type strain by DNA-DNA hybridization (33.3 %), digital DNA-DNA hybridization (21.2 %), average nucleotide identity (75.7 %) and by a range of physiological and biochemical characteristics. Strain 130T contained MK-8(H4) and MK-7 as the major menaquinones, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol as the main polar lipids, and iso-C16 : 0, C17 : 1ω8c, anteiso-C17 : 0, C18 : 1ω9c, C17 : 0 and iso-C14 : 0 as the major cellular fatty acids. The novel strain grew at 20-36 °C, at pH 6.0-8.0 and in the presence of 0-6 % (w/v) NaCl. The genomic DNA G+C content was 72.9 mol%. The genome contained 4817 putative protein-coding sequences, and 45 tRNA and three rRNA genes. Phylogenomic analysis confirmed that strain 130T belongs to the genus Nocardioides and distinguished it from recognized Nocardioides species with available genomes. Based on these polyphasic taxonomic data, strain 130T represents a new species of the genus Nocardioides, for which the name Nocardioidesguangzhouensis sp. nov. is proposed. The type strain is 130T (=CICC 24668T=JCM 33269T).

DeepMineLys: Deep mining of phage lysins from human microbiome.

Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.

Application of the molecular dynamics simulation GROMACS in food science.

Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.

Evaluation of Guidelines and Consensus on Ectopic Pregnancy Based by AGREE II Method.

Introduction: To evaluate the methodological quality of diagnosis and treatment guidelines/consensus related to ectopic pregnancy. Materials and methods: Use the "Appraisal of Guidelines and Research and Evaluation" (AGREE II) method to evaluate the differences among the guideline/consensus. Results: We appraised 9 clinical practice guidelines for ectopic pregnancy (9 clinical practice guidelines from 5 countries) including the United States, United Kingdom, Ireland, Canada, and China. The guidelines received the highest scores for clarity of presentation (82.72%) and lowest scores for editorial independence (30.56%). The comprehensive recommendations of the 7 guidelines were Grade B, the other 2 guidelines were Grade C. Conclusion: The overall quality of the ectopic pregnancy guidelines had room for improvement. It is recommended to supplement and improve the four fields of "independence", "rigor", "participants" and "application", especially the "independence" and "application" fields.

A robust thorium-organic framework as a bifunctional platform for iodine adsorption and Cr(VI) sensitization.

Simple synthetic modulation based on thorium nitrate and tris((4-carboxyl)phenylduryl)amine (H3TCBPA) gives rise to a new thorium-based metal-organic framework, Th-TCBPA, which features excellent hydrolytic and thermal stabilities. Incorporating electron-rich TCBPA3- linkers not only endows Th-TCBPA with high adsorption capacity toward radioiodine vapor, but also makes it a luminescence sensor for the highly sensitive and selective detection of Cr(VI) anions.