The <scp>ImageJ</scp> ecosystem: Open‐source software for image visualization, processing, and analysis

Intermediate filaments are integral components of the cytoskeleton in metazoan cells. Due to their specific viscoelastic properties they are principal contributors to flexibility and tear strength of cells and tissues. Vimentin, an intermediate filament protein expressed in fibroblasts and endothelial cells, assembles into ~11 nm thick biopolymers, that are involved in a wide variety of cellular functions in health and disease. Here, we reveal the structure of in-situ polymerized vimentin filaments to a subnanometer resolution by applying cryo-electron tomography to mouse embryonic fibroblasts grown on electron microscopy grids. We show that vimentin filaments are tube-like assemblies with a well-defined helical symmetry. Their structure is comprised of five octameric, spring-like protofibrils harboring 40 vimentin polypeptide chains in cross-section. The protofibrils are connected by the intrinsically disordered head and helix 1A domains of vimentin. Individual filaments display two polymerization states characterized by either the presence or absence of a luminal density along the helical axis. The structure of vimentin filaments unveils the generic building plan of the intermediate filament superfamily in molecular details.

show abstract

“…Subsequently, the assembled VIFs were unbent based on a MATLAB algorithm derived from the ImageJ 64 straighten function 1,54 .…”

Section: Discussionmentioning

confidence: 99%

The molecular architecture of vimentin filaments

Eibauer

Weber

Turgay

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Briefly, each well of 96-well plate was placed into five 72 hpf (hour of post-fertilization) larvae with 200 μL E3 water containing test compounds. The larvae were maintained for 1 h and then treated with 2-NBDG (0.6 mM) for a further 3 h. After being washed using E3 water and anesthetized using 0.25% tricaine, the larvae were captured on fluorescence microscopy, and the uptake of 2-NBDG was quantified using Fiji (ImageJ) following a standard method [ 39 ].…”

Section: Methodsmentioning

confidence: 99%

Insulin-Mimic Components in Acer truncatum Leaves: Bio-Guided Isolation, Annual Variance Profiling and Regulating Pathway Investigated by Omics

Zhang

Liu

et al. 2021

Pharmaceuticals

View full text Add to dashboard Cite

Insulin mimic can promote transporting glucose to muscle tissue and accelerate glucose consumption. It is commonly occurring in many functional foods or traditional medicines. Anti-diabetes molecules from food sources are highly safe and suitable for long-term use to prevent early diabetes. The leaves of Acer truncatum was found glucose uptake promotion in our phenotypic screening. However, its bioactive components and mechanism are still unclear. We collected leaves from trees of different ages (2, 3, 4, 7 and 11 years old) and profiled the ingredients by LC-MS/MS. The essential active component (myricitrin) was acquired following bio-guide on a whole organism Zebrafish (Danio rerio). Its content in the leaves was not affected by tree ages. Therefore, myricitrin can serve as a quality mark for functional foods derived from A. truncatum leaves. The transcriptomic and metabolomic analysis in Zebrafish explored the differentially expressed genes and metabolites. Based on joint-pathway enrichment and qRT-PCR verification, the critical bioactive component myricitrin was found to affect toll-like receptors signaling pathways to regulate glucose uptake. Our findings disclosed a bioactive marker (myricitrin) in A. truncatum leaves and explored its regulation mechanism, which rationalized the anti-diabetes function of the herbal food.

show abstract

“…A heatmap of changes in relevant bacteria was made using QIIME2/2017.10. Values from the heatmap for statistical analysis were reconstructed using ImageJ software [ 53 ].…”

Section: Methodsmentioning

confidence: 99%

Gut Microbiota Regulates the Interaction between Diet and Genetics to Influence Glucose Tolerance

et al. 2021

View full text Add to dashboard Cite

Background: Metabolic phenotypes are the result of an intricate interplay between multiple factors, including diet, genotype, and the gut microbiome. Per–Arnt–Sim (PAS) kinase is a nutrient-sensing serine/threonine kinase, whose absence (PASK−/−) protects against triglyceride accumulation, insulin resistance, and weight gain on a high-fat diet; conditions that are associated with dysbiosis of the gut microbiome. Methods: Herein, we report the metabolic effects of the interplay of diet (high fat high sugar, HFHS), genotype (PASK−/−), and microbiome (16S sequencing). Results: Microbiome analysis identified a diet-induced, genotype-independent forked shift, with two discrete clusters of HFHS mice having increased beta and decreased alpha diversity. A “lower” cluster contained elevated levels of Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Defferibacteres, and was associated with increased weight gain, glucose intolerance, triglyceride accumulation, and decreased claudin-1 expression. Genotypic effects were observed within the clusters, lower cluster PASK−/− mice displayed increased weight gain and decreased triglyceride accumulation, whereas upper PASK−/− were resistant to decreased claudin-1. Conclusions: These results confirm previous reports that PAS kinase deficiency can protect mice against the deleterious effects of diet, and they suggest that microbiome imbalances can override protection. In addition, these results support a healthy diet for beneficial microbiome maintenance and suggest microbial culprits associated with metabolic disease.

show abstract

The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis

Cited by 135 publications

References 81 publications

The molecular architecture of vimentin filaments

The molecular architecture of vimentin filaments

Insulin-Mimic Components in Acer truncatum Leaves: Bio-Guided Isolation, Annual Variance Profiling and Regulating Pathway Investigated by Omics

Gut Microbiota Regulates the Interaction between Diet and Genetics to Influence Glucose Tolerance

Contact Info

Product

Resources

About