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Structural Determination of the Polycystin-2 Channel by Electron Cryo-Microscopy
Published in Jinghua Hu, Yong Yu, Polycystic Kidney Disease, 2019
Before mounting the sample onto a transmission electron microscope for imaging, the protein sample has to be spotted onto a solid support and preserved in a native-like, frozen hydrated state within a thin layer of vitreous ice. The cryo-EM sample grids, the solid support, is typically made from copper or gold. A thin layer of amorphous carbon is coated on one side of the copper grid, but often with regularly arrayed perforations (or holes) where a thin layer of vitreous ice with embedded biological molecules will form. As the carbon support film is hydrophobic in nature, a glow discharge treatment is needed to deposit negative charges on the carbon film, thus making it hydrophilic so that the applied protein sample can spread evenly across the grid.
Data Collection Methods
Published in Kitsakorn Locharoenrat, Research Methodologies for Beginners, 2017
The second harmonic intensity from the Au, Cu, and Pt nanowire arrays was measured as a function of the sample rotation angle φ at the photon energy of 1.17 eV for Au and Cu and at the photon energy of 2.33 eV for Pt. The angle ϕ was defined as the angle between the incident plane and the wire axes in the [001] substrate direction. The measurements were carried out in four different input/output polarization combinations: p-in/p-out, p-in/s-out, s-in/p-out, and s-in/s-out. The sample preparation method was shadow deposition and outlined as in [9]. The minimum widths of the obtained nanowires were 40 nm for Au, 14 nm for Cu, and 9 nm for Pt. By using this shadow deposition technique, we obtained the large areas of very thin samples and we could perform the transmission electron microscopy and optical experiments at different points in each sample as well as compare the obtained data statistically. Furthermore, the ridge-and-valley surface morphology was considered to be preserved well even after the deposition of amorphous SiO overlayer, as confirmed for amorphous carbon overlayer by the AFM study [10].
Inorganic Particulates in Human Lung: Relationship to the Inflammatory Response
Published in William S. Lynn, Inflammatory Cells and Lung Disease, 2019
Victor L. Roggli, J. P. Mastin, John D. Shelburne, Michael Roe, Arnold R. Brody
Elemental or inorganic carbon occurs in three basic forms. Diamond consists of carbon atoms in a tetrahedral arrangement, with each carbon atom bound to four adjacent carbon atoms. Graphite consists of loosely bound sheets of carbon atoms, with the atoms within the plane of each sheet arranged in a hexagonal pattern. The third form, amorphous carbon, originates from decaying organic matter and forms the familiar material we know as coal. It is also a major component of smoke from combustion of any organic material. Amorphous carbon probably accounts for the bulk of the material known as anthracotic pigment, which may be found in the lung parenchyma and hilar lymph nodes of virtually all adult lungs.113 The pigment is distributed in the interstitium along the pathway of lymphatics, especially beneath the pleura, and virtually all of it is found within macrophages as particles ranging up to approximately 3 µ in greatest dimension. The degree of pigmentation of the lung increases with age, although there is a marked variation in pigmentation which is probably related to individual differences with respect to deposition and clearance of particulate material in the lung.114 Cigarette smokers’ lungs as a group contain more pigment than the lungs of non-smokers, although there is considerable overlap between the two groups. In addition, emphysematous lungs contain more pigment than non-emphysematous lungs, and there appears to be a greater concentration of pigment in the emphysematous areas of lungs from individuals with centrilobular emphysema than in the more normal regions of the same lungs.115 Accumulation of groups of anthracotic pigment-laden macrophages within the alveolar spaces and peribronchiolar interstitium of the lung constitute the macular lesion, which is the morphologic hallmark of simple coal workers’ pneumoconiosis.113
The sp3/sp2 carbon ratio as a modulator of in vivo and in vitro toxicity of the chemically purified detonation-synthesized nanodiamond via the reactive oxygen species generation
Published in Nanotoxicology, 2020
Dong-Keun Lee, Sangwook Ha, Soyeon Jeon, Jiyoung Jeong, Dong-Jae Kim, Seung Whan Lee, Wan-Seob Cho
As reference materials, amorphous carbon black (CB) and nickel oxide (NiO) were selected as a non-diamond structured carbon particle and high toxicity particle, respectively. Because nanomaterials tend to agglomerate, DND samples and reference materials were well-dispersed before experiments according to the previously described method (Cho et al. 2010). Briefly, the stock solution of nanomaterials was dispersed in distilled water (DW) at 10-fold higher concentration of working concentration and sonicated for 5 min in a bath sonicator (Saehan Sonic, Seoul, Korea). Then, heat-inactivated alloantigenic rat serum as a dispersion medium was added at 3% v/v for working concentration and sonicated for 5 min. The working solution was prepared by the addition of sterile phosphate-buffered saline (PBS).
N6-methyladenosine-dependent primary microRNA-126 processing activated PI3K-AKT-mTOR pathway drove the development of pulmonary fibrosis induced by nanoscale carbon black particles in rats
Published in Nanotoxicology, 2020
Bin Han, Chen Chu, Xuan Su, Ning Zhang, Lixiao Zhou, Mengyue Zhang, Shuaishuai Yang, Lei Shi, Bo Zhao, Yujie Niu, Rong Zhang
Carbon black (CB) is a kind of amorphous carbon produced by incomplete combustion or thermal cracking of hydrocarbons under conditions of insufficient air. CB is widely used due to its good stability and inertness, such as black dye for the manufacture of inks, paints, and reinforcing agent for rubber. In toxicological study, CB is often used as a negative control because of its low toxicity and low solubility (Hubbs et al. 2013). However, study has shown that CB could induce inflammation and histopathological damage in lung (Koike et al. 2008). CB was thought to exacerbate several respiratory diseases in humans, including lung inflammation and fibrosis (Lin et al. 2011; Kamata et al. 2011; Saputra et al. 2014). In our previous study, we found the thickening of the alveolar wall and collagen deposition after CB inhalation for 14 days in mice (Zhang et al. 2014). Though the fibrosis in lung could be induced by CB particles, the mechanism of fibrosis has not been known clearly. ‘PI3K/AKT/mTOR signaling pathway’ plays an important role in regulating physiological functions such as cell growth, proliferation, cell survival, protein synthesis and transcription (Hay and Sonenberg 2004). Previous studies suggested the PI3K/AKT/mTOR signaling pathway was involved in the development of fibrotic diseases, such as cardiac fibrosis (Yu et al. 2013; Han et al. 2006), liver fibrosis (Patsenker et al. 2011) and renal fibrosis (Geissler and Schlitt 2010). mTOR inhibitors showed fibrotic intervention on pulmonary fibrosis in both of human (Luai et al. 2014) and animals (Bartel 2009; Brennecke et al. 2003; Liu et al. 2010). p70S6k has been shown to be downstream of mTOR, which reflect activation of the mTOR signaling pathway (Brown et al. 1995; Dennis, Fumagalli, and Thomas 1999).
Inner surface modification of ureteral stent polyurethane tubes based by plasma-enhanced chemical vapor deposition to reduce encrustation and biofilm formation
Published in Biofouling, 2022
Hyuna Lim, Jae Hoon Chung, Yoonsoo Park, Namwuk Baek, Youngsik Seo, Heonyong Park, Yong Ki Cho, Donggeun Jung, Deok Hyun Han
Generally, amorphous carbon films are analyzed in the range of 800–2,000 cm−1. As a result of the deconvoluted Raman spectra of PU(C2H2), the G peak (single-crystal graphite band) and D peak (disordered graphite band) appeared at 1,560 and 1,380 cm−1, respectively. The ratio of the D peak intensity to the G peak intensity, ID/IG, is an index of the degree of defect in the C bond structure, and ID/IG ∼ 0.45 for PU(C2H2) represents the ratio of a typical amorphous carbon film (Figure 7).