Search

Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p

Background/Objectives: Limosilactobacillus (Lm.) reuteri is a widely utilized probiotic, recognized for its significant role in alleviating symptoms associated with gastrointestinal and psychiatric disorders. However, the effectiveness of Lm. reuteri is strain-specific, and its genetic diversity leads to significant differences in phenotypes among different strains. This study aims to identify potential probiotic strains by comparing the strain-specific characteristics of Lm. reuteri to better understand their efficacy and mechanisms in alleviating stress-induced anxiety-like behaviors and gastrointestinal symptoms. Methods: We cultivated 11 strains of Lm. reuteri from healthy human samples and conducted phenotypic and genomic characterizations. Two strains, WLR01 (=GOLDGUT-LR99) and WLR06, were screened as potential probiotics and were tested for their efficacy in alleviating anxiety-like behavior and intestinal symptoms in mouse models subjected to sleep deprivation (SD) and water avoidance stress (WAS). Results: The results showed that the selected strains effectively improved mouse behaviors, including cognitive impairment and inflammatory response, as well as improving anxiety and regulating gut microbiota composition. The improvements with WLR01 were associated with the regulation of the NLRP3 inflammasome pathway in the SD model mice and were associated with visceral hypersensitivity and intestinal integrity in the WAS model mice. Conclusions: In summary, this study identified the Lm. reuteri strain WLR01 as having the potential to alleviate anxiety-like behavior and intestinal symptoms through the analysis of Lm. reuteri genotypes and phenotypes, as well as validation in mouse models, thereby laying the foundation for future clinical applications. [ABSTRACT FROM AUTHOR]

Glycosylation and phosphorylation rank as paramount post‐translational modifications, and their analysis heavily relies on enrichment techniques. In this work, a facile approach was developed for the one‐step simultaneous enrichment and stepwise elution of glycoproteins and phosphoproteins. The core of this approach was the application of the novel titanium (IV) ion immobilized poly(glycidyl methacrylate) microparticles functionalized with dendrimer polyethylenimine and phytic acid. The microparticles possessed dual enrichment capabilities due to their abundant titanium ions and hydroxyl groups on the surface. They demonstrate rapid adsorption equilibrium (within 30 min) and exceptional adsorption capacity for β‐casein (1107.7 mg/g) and horseradish peroxidase (438.6 mg/g), surpassing that of bovine serum albumin (91.7 mg/g). Furthermore, sodium dodecyl sulfate‐polyacrylamide gel electrophoresis was conducted to validate the enrichment capability. Experimental results across various biological samples, including standard protein mixtures, non‐fat milk, and human serum, demonstrated the remarkable ability of these microparticles to enrich low‐abundance glycoproteins and phosphoproteins from biological samples. [ABSTRACT FROM AUTHOR]

Spatial transcriptomics (ST) technologies allow researchers to examine transcriptional profiles along with maintained positional information. Such spatially resolved transcriptional characterization of intact tissue samples provides an integrated view of gene expression in its natural spatial and functional context. However, high-throughput sequencing-based ST technologies cannot yet reach single cell resolution. Thus, similar to bulk RNA-seq data, gene expression data at ST spot-level reflect transcriptional profiles of multiple cells and entail the inference of cell-type composition within each ST spot for valid and powerful subsequent analyses. Realizing the critical importance of cell-type decomposition, multiple groups have developed ST deconvolution methods. The aim of this work is to review state-of-the-art methods for ST deconvolution, comparing their strengths and weaknesses. In particular, we construct ST spots from single-cell level ST data to assess the performance of 10 methods, with either ideal reference or non-ideal reference. Furthermore, we examine the performance of these methods on spot- and bead-level ST data by comparing estimated cell-type proportions to carefully matched single-cell ST data. In comparing the performance on various tissues and technological platforms, we concluded that RCTD and stereoscope achieve more robust and accurate inferences. [ABSTRACT FROM AUTHOR]

The three-dimensional organization of chromatin plays a critical role in gene regulation. Recently developed technologies, such as HiChIP and proximity ligation-assisted ChIP-Seq (PLAC-seq) (hereafter referred to as HP for brevity), can measure chromosome spatial organization by interrogating chromatin interactions mediated by a protein of interest. While offering cost-efficiency over genome-wide unbiased high-throughput chromosome conformation capture (Hi-C) data, HP data remain sparse at kilobase (Kb) resolution with the current sequencing depth in the order of 108 reads per sample. Deep learning models, including HiCPlus, HiCNN, HiCNN2, DeepHiC and Variationally Encoded Hi-C Loss Enhancer (VEHiCLE), have been developed to enhance the sequencing depth of Hi-C data, but their performance on HP data has not been benchmarked. Here, we performed a comprehensive evaluation of HP data sequencing depth enhancement using models developed for Hi-C data. Specifically, we analyzed various HP data, including Smc1a HiChIP data of the human lymphoblastoid cell line GM12878, H3K4me3 PLAC-seq data of four human neural cell types as well as of mouse embryonic stem cells (mESC), and mESC CCCTC-binding factor (CTCF) PLAC-seq data. Our evaluations lead to the following three findings: (i) most models developed for Hi-C data achieve reasonable performance when applied to HP data (e.g. with Pearson correlation ranging 0.76–0.95 for pairs of loci within 300 Kb), and the enhanced datasets lead to improved statistical power for detecting long-range chromatin interactions, (ii) models trained on HP data outperform those trained on Hi-C data and (iii) most models are transferable across cell types. Our results provide a general guideline for HP data enhancement using existing methods designed for Hi-C data. [ABSTRACT FROM AUTHOR]

Glycosylation and phosphorylation rank as paramount post-translational modifications, and their analysis heavily relies on enrichment techniques. In this work, a facile approach was developed for the one-step simultaneous enrichment and stepwise elution of glycoproteins and phosphoproteins. The core of this approach was the application of the novel titanium (IV) ion immobilized poly(glycidyl methacrylate) microparticles functionalized with dendrimer polyethylenimine and phytic acid. The microparticles possessed dual enrichment capabilities due to their abundant titanium ions and hydroxyl groups on the surface. They demonstrate rapid adsorption equilibrium (within 30 min) and exceptional adsorption capacity for β-casein (1107.7 mg/g) and horseradish peroxidase (438.6 mg/g), surpassing that of bovine serum albumin (91.7 mg/g). Furthermore, sodium dodecyl sulfate-polyacrylamide gel electrophoresis was conducted to validate the enrichment capability. Experimental results across various biological samples, including standard protein mixtures, non-fat milk, and human serum, demonstrated the remarkable ability of these microparticles to enrich low-abundance glycoproteins and phosphoproteins from biological samples., (© 2024 Wiley‐VCH GmbH.)

Aquatic plants and the epiphytic microorganisms are important contributors to the purification of constructed wetlands. Taking the dragon-shaped water system of Beijing Olympic Park as a model, this study analyzed the structure and function of the microbial communities reside the sediment, the water body and the rhizosphere and phyllosphere of three submerged plants-Vallisneria natans, Myriophyllum verticillatum, and Potamogeton pectinatus using high-throughput sequencing technology. The results showed that the microbial diversity from the highest to the lowest were samples from sediment, plant rhizosphere, plant phyllosphere and water. The microbial diversity of plant phyllosphere samples were significantly higher than those of the water body. LEfSe analysis showed that different habitats enriched different microbial groups. The sediments mainly enriched anaerobic microbes, while the water body and the phyllosphere of plants mainly enriched aerobic microbes, and the rhizosphere of plants had the both. Functional prediction analysis showed that the abundance of denitrification marker genes in phyllosphere samples was higher than that in samples from rhizosphere, sediment and water body, and the abundance of denitrification marker genes in phyllosphere samples of M. verticillatum and P. pectinatus was higher than that of V. natans. This study could serve as a guidance for the selection of submerged plants and functional microorganisms for constructed wetlands.

Co-crystallizing iodine with a simple dicationic salt (1,8-diammoniumoctane chloride) results in the clathration of the iodine (I 2 ) molecules inside trigonal and hexagonal helical channels of the crystal lattice with 72 wt % overall I 2 loading. The I 2 inside the bigger trigonal channel forms a I-I⋅⋅⋅I-I⋅⋅⋅I-I halogen-bonded infinite helical chain, while the I 2 in the smaller hexagonal channel is disordered. In both channels the I 2 interaction with the channel wall happens through I-I⋅⋅⋅Cl - halogen bonds. The helical channels in the crystal lattice are constructed via the strong charge-assisted H 2 N + H⋅⋅⋅Cl - hydrogen bonds between the dications and the chloride anions. The structure shows a marked similarity with the well-known starch-I 2 system, and thus may provide insight for the yet unresolved structure of the I 2 in the helical starch channel., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)