Alternative Splicing Is a Major Factor Shaping Transcriptome Diversity in Mild and Severe Chronic Obstructive Pulmonary Disease.

The role of alternative splicing in chronic obstructive pulmonary disease (COPD) is still largely unknown. We aimed to investigate the differences in alternatively splicing events between patients with mild-to-moderate and severe COPD compared with non-COPD control subjects and to identify splicing factors associated with aberrant alternative splicing in COPD. For this purpose, we performed genome-wide RNA-sequencing analysis of bronchial brushings from 23 patients with mild-to-moderate COPD, 121 with severe COPD, and 23 non-COPD control subjects. We found a significant difference in the frequency of alternative splicing events in patients with mild-to-moderate and severe COPD compared with non-COPD control subjects. There were from two to eight times (depending on event type) more differential alternative splicing events in the severe than in the mild-to-moderate stage. The severe COPD samples showed less intron retention and more exon skipping. It is interesting that the transcript levels of the top 10 differentially expressed splicing factors were significantly correlated with the percentage of many alternatively spliced transcripts in severe COPD. The aberrant alternative splicing in severe COPD was predicted to increase the overall protein-coding capacity of gene products. In conclusion, we observed large and significant differences in alternative splicing between bronchial samples of patients with COPD and control subjects, with more events observed in severe than in mild-to-moderate COPD. The changes in the expression of several splicing factors correlated with prevalence of alternative splicing in severe COPD. Alternative splicing can indirectly impact gene expression by changing the relative abundance of protein-coding isoforms potentially influencing pathophysiological changes. The results provide a better understanding of COPD-related alternative splicing changes.

An epithelial gene signature of trans-IL-6 signaling defines a subgroup of type 2-low asthma.

BACKGROUND: Asthma is stratified into type 2-high and type 2-low inflammatory phenotypes. Limited success has been achieved in developing drugs that target type 2-low inflammation. Previous studies have linked IL-6 signaling to severe asthma. IL-6 cooperates with soluble-IL-6Rα to activate cell signaling in airway epithelium. OBJECTIVE: We sought to study the role of sIL-6Rα amplified IL-6 signaling in airway epithelium and to develop an IL-6+ sIL-6Rα gene signature that may be used to select asthma patients who potentially respond to anti-IL-6 therapy. METHODS: Human airway epithelial cells were stimulated with combinations of IL-6, sIL-6Rα, and inhibitors, sgp130 (Olamkicept), and anti-IL-6R (Tocilizumab), to assess effects on pathway activation, epithelial barrier integrity, and gene expression. A gene signature was generated to identify IL-6 high patients using bronchial biopsies and nasal brushes. RESULTS: Soluble-IL-6Rα amplified the activation of the IL-6 pathway, shown by the increase of STAT3 phosphorylation and stronger gene induction in airway epithelial cells compared to IL-6 alone. Olamkicept and Tocilizumab inhibited the effect of IL-6 + sIL-6Rα on gene expression. We developed an IL-6 + sIL-6Rα gene signature and observed enrichment of this signature in bronchial biopsies but not nasal brushes from asthma patients compared to healthy controls. An IL-6 + sIL-6Rα gene signature score was associated with lower levels of sputum eosinophils in asthma. CONCLUSION: sIL-6Rα amplifies IL-6 signaling in bronchial epithelial cells. Higher local airway IL-6 + sIL-6Rα signaling is observed in asthma patients with low sputum eosinophils.

Lactoferrin translocates to the nucleus of bovine rectal epithelial cells in the presence of Escherichia coli O157:H7.

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen which causes illness in humans. Ruminants are the main reservoirs and EHEC predominantly colonizes the epithelium of the recto-anal junction of cattle. Immunosuppression by EHEC promotes re-infection of cattle. However, bovine lactoferrin (bLF) apparently can overrule the immunosuppression by inducing EHEC-specific IgA responses at the mucosal site. The IgA responses are significantly correlated with reduced EHEC shedding and the absence of colonization at the rectal mucosa following re-infection. Therefore, to examine the interaction between bLF and bovine rectal epithelial cells, we first developed a method to establish a primary cell culture of epithelial cells of the rectum of cattle. Furthermore, we used LC-MS/MS to demonstrate the presence of secreted lactoferrin in bovine milk and the absence of a "delta" isoform which is known to translocate to the nucleus of cells. Nevertheless, lactoferrin derived from bovine milk was internalized by rectal epithelial cells and translocated to the nuclei. Moreover, nuclear translocation of bLF was significantly enhanced when the epithelial cells were inoculated with EHEC, as demonstrated by confocal fluorescence microscopy and confirmed by Raman microscopy and 3D imaging.

Superresolution 4π Raman microscopy.

The advent of 4π microscopy broke the conventional optical resolution limit in the axial direction of the microscope. In combination with fluorescence microscopy, it broadened the knowledge of cell biology at the expense of perturbing the samples with extrinsic fluorescent labels. In contrast, Raman microscopy acquires the molecular fingerprint of the sample without the need of extrinsic labels, and therefore improving its resolution can make an even greater impact. Here, we take advantage of the improved axial resolution of a 4π configuration to form a 4π Raman microscope. With this microscope, we independently and simultaneously analyzed different nanolayers in a multilayer stack. We identified their chemical composition and retrieved their relative subwavelength optical separation with a precision of 6 nm.

Chlamydia psittaci infected cell studies by 4Pi Raman and atomic force microscopy.

Chlamydia psittaci is an avian bacterial pathogen that can cause atypical pneumonia in humans via zoonotic transmission. It is a Gram-negative intracellular bacterium that proliferates inside membrane bound inclusions in the cytoplasm of living eukaryotic cells. The study of such cells with C. psittaci inside without destroying them poses a significant challenge. We demonstrated in this work the utility of a combined multitool approach to analyze such complex samples. Atomic force microscopy was applied to obtain high-resolution images of the surface of infected cells upon entrance of bacteria. Atomic force microscopy scans revealed the morphological changes of the cell membrane of Chlamydia infected cells such as changes in roughness of cell membrane and the presence of micro vesicles. 4Pi Raman microscopy was used to image and probe the molecular composition of intracellular bacteria inside intact cells. Information about the structure of the inclusion produced by C. psittaci was obtained and it was found to have a similar molecular fingerprint as that of an intracellular lipid droplet but with less proteins and unsaturated lipids. The presented approach demonstrates complementarity of various microscopy-based approaches and might be useful for characterization of intracellular bacteria.

Efficient long-range conduction in cable bacteria through nickel protein wires.

Filamentous cable bacteria display long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron transport mechanism remain unresolved. Here, we combine high-resolution microscopy, spectroscopy, and chemical imaging on individual cable bacterium filaments to demonstrate that the periplasmic wires consist of a conductive protein core surrounded by an insulating protein shell layer. The core proteins contain a sulfur-ligated nickel cofactor, and conductivity decreases when nickel is oxidized or selectively removed. The involvement of nickel as the active metal in biological conduction is remarkable, and suggests a hitherto unknown form of electron transport that enables efficient conduction in centimeter-long protein structures.

Water-Stable Plasma-Polymerized N,N-Dimethylacrylamide Coatings to Control Cellular Adhesion.

The plasma polymerization of amide-based precursors is a nearly unexplored research area, which is in contrast with the abundance of reports focusing on amide-based surface modification using wet chemistry. Therefore, this study aims to profoundly investigate the near-atmospheric pressure plasma polymerization of N,N-dimethylacrylamide (DMAM) to obtain stable coatings. In contrast to the unstable coatings obtained at lower discharge powers, the stable coatings that were obtained at higher powers showed a lower hydrophilicity as assessed by water contact angle (WCA). This decrease in hydrophilicity with increasing plasma power was found to be related to a reduced preservation of the monomer structure, as observed by Fourier transform infrared (FTIR), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and XPS C60 depth profiling, a rarely used but effective combination of techniques. Furthermore, the chemical composition of the coating was found to be in good agreement with the plasma active species observed by optical emission spectroscopy. Additionally, XPS C60 depth profiling indicated a difference between the top layer and bulk of the plasma polymer due to spontaneous oxidation and/or postplasma coating deposition. Finally, the stable coatings were also found to have cell-interactive behavior toward MC3T3 as studied by in vitro live/dead fluorescence imaging and (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) (MTS) assays. With the latter technique, a cell viability of up to 89% as compared with tissue culture plates after 1 day of cell culture was observed, indicating the potential of these coatings for tissue engineering purposes.

Modulating the crystallization of phytosterols with monoglycerides in the binary mixture systems: mixing behavior and eutectic formation.

Phytosterols (PSs) are insoluble in water and poorly soluble in oil, which hampers their potential as cholesterol level regulator in human. To mitigate this problem, monoglycerides (MGs) were used to modulates the crystallization behavior of PSs. Therefore, the understanding on mixing behavior provides the insight into different aspects of crystallization and the resultant effects. The effects on thermal, morphology, diffraction, and spectroscopy behavior were investigated for binary mixtures of 11 different ratios (100:0 to 0:100 MGs:PSs). The phase behavior of binary mixtures of commercial MGs and PSs exhibited complexity with the formation of eutectic mixtures at 90:10 and 80:20 (MGs:PSs) combinations. These combinations revealed a single melting profile and reduced melting enthalpy, though after a month of storage at 5 °C. Conversely, two separate melting regions were observed in others. Furthermore, powder X-ray diffraction (PXRD) analysis of selected combinations revealed a change in crystalline forms with changes in the peaks located between 18-19° (2θ) and 25-26° (2θ). Accordingly, Raman spectroscopy results revealed changes in intensities and peak shape. Therefore, the change in crystalline forms or behavior correlated well to the change in thermal properties. Overall, the characterizations revealed the formation of eutectic mixtures between MGs and PSs at 90:10 and 80:20 (MGs:PSs) in which MGs modified the crystallization of PSs and changed the crystal forms thus, thermal behaviors. This study provides new insight into the mixing behavior of MGs and PSs which supports other research. Therefore, the results of this study are beneficial for the improvement of formulation of phytosterols in food and pharmaceutical products. Nonetheless, this study reveals a simple technique to alter crystal forms of phytosterols through simple complexation with monoglycerides.

Label-free Raman characterization of bacteria calls for standardized procedures.

Raman spectroscopy has gained relevance in single-cell microbiology for its ability to detect bacterial (sub)populations in a non-destructive and label-free way. However, the Raman spectrum of a bacterium can be heavily affected by abiotic factors, which may influence the interpretation of experimental results. Additionally, there is no publicly available standard for the annotation of metadata describing sample preparation and acquisition of Raman spectra. This article explores the importance of sample manipulations when measuring bacterial subpopulations using Raman spectroscopy. Based on the results of this study and previous findings in literature we propose a Raman metadata standard that incorporates the minimum information that is required to be reported in order to correctly interpret data from Raman spectroscopy experiments. Its aim is twofold: 1) mitigate technical noise due to sample preparation and manipulation and 2) improve reproducibility in Raman spectroscopy experiments studying microbial communities.

Laser-induced remote release in vivo in C. elegans from novel silver nanoparticles-alginate hydrogel shells.

Non-destructive, controllable, remote light-induced release inside cells enables studying time- and space-specific processes in biology. In this work we demonstrate the remote release of tagged proteins in Caenorhabditis elegans (C. elegans) worms using a near-infrared laser light as a trigger from novel hydrogel shells functionalized with silver nanoparticles responsive to laser light. A new type of hydrogel shells was developed capable of withstanding prolonged storage in the lyophilized state to enable the uptake of the shell by worms, which takes place on an agar plate under standard culture conditions. Uptake of the shells by C. elegans was confirmed using confocal laser scanning microscopy, while release from alginate shells in C. elegans and the laser effect on the shells on a substrate in air was followed using fluorescence microscopy. In addition, Raman microscopy was used to track the localization of particles to avoid the influence of autofluorescence. Hierarchical cluster spectral analysis is used to extract information about the biochemical composition of an area of a nematode containing the hydrogel shells, whose Raman signal is enhanced by the SERS (Surface Enhanced Raman Scattering) effect due to hot spots formed by silver nanoparticles present in the shells. The in vivo release demonstrated here can be used to study intestinal microbiota and probiotic compounds as well as a possible future strategy for gene delivery in the worms, other insects and other organisms.

Transfer of cells with uptaken nanocomposite, magnetite-nanoparticle functionalized capsules with electromagnetic tweezers.

Targeted cell delivery via magnetically sensitive microcapsules of an applied magnetic field would advance localized cell transplantation therapy, by which healthy cells can be introduced into tissues to repair damaged or diseased organs. In the present research, we implement magnetically sensitive cells via an uptake of microcapsules containing magnetic nanoparticles in their walls. As is shown in an example of the MA-104 cell line, the magnetic polyelectrolyte multilayer capsules have no toxicity effect on the cells after internalization. Microscopy methods have been used to evaluate the uptake of capsules by the cells. Magnetically sensitive cells are retained in the capillary flow when the magnetic gradient field is applied (<200 T m-1), but they proliferate at the site of retention for several days after the magnet is removed. As an example of cell manipulation, we have demonstrated a novel methodology for cell sheet isolation and transfer using cells impregnated with magnetic microcapsules. A weak enzyme treatment is used to facilitate tissue engineering assemblies by cell monolayer deposition. This type of cell monolayer assembly has provided a 3D tissue engineering construction using an externally applied magnetic field, which is modelled in this study. The approach presented in this work opens perspectives for preclinical studies of tissue and organ repair.

Novel self-gelling injectable hydrogel/alpha-tricalcium phosphate composites for bone regeneration: Physiochemical and microcomputer tomographical characterization.

Mineralized hydrogels are increasingly gaining attention as biomaterials for bone regeneration. The most common mineralization strategy has been addition of preformed inorganic particles during hydrogel formation. This maintains injectability. One common form of bone cement is formed by mixing particles of the highly reactive calcium phosphate alpha-tricalcium phosphate (α-TCP) with water to form hydroxyapatite (HA). The calcium ions released during this reaction can be exploited to crosslink anionic, calcium-binding polymers such as the polysaccharide gellan gum (GG) to induce hydrogel formation. In this study, three different amounts of α-TCP particles were added to GG polymer solution to generate novel, injectable hydrogel-inorganic composites. Distribution of the inorganic phase in the hydrogel was studied by high resolution microcomputer tomography (µCT). Gelation occurred within 30 min. α-TCP converted to HA. µCT revealed inhomogeneous distribution of the inorganic phase in the composites. These results demonstrate the potential of the composites as alternatives to traditional α-TCP bone cement and pave the way for incorporation of biologically active substances and in vitro and in vivo testing. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 822-828, 2018.

Ca:Mg:Zn:CO3 and Ca:Mg:CO3-tri- and bi-elemental carbonate microparticles for novel injectable self-gelling hydrogel-microparticle composites for tissue regeneration.

Injectable composites for tissue regeneration can be developed by dispersion of inorganic microparticles and cells in a hydrogel phase. In this study, multifunctional carbonate microparticles containing different amounts of calcium, magnesium and zinc were mixed with solutions of gellan gum (GG), an anionic polysaccharide, to form injectable hydrogel-microparticle composites, containing Zn, Ca and Mg. Zn and Ca were incorporated into microparticle preparations to a greater extent than Mg. Microparticle groups were heterogeneous and contained microparticles of differing shape and elemental composition. Zn-rich microparticles were 'star shaped' and appeared to consist of small crystallites, while Zn-poor, Ca- and Mg-rich microparticles were irregular in shape and appeared to contain lager crystallites. Zn-free microparticle groups exhibited the best cytocompatibility and, unexpectedly, Zn-free composites showed the highest antibacterial activity towards methicilin-resistant Staphylococcus aureus. Composites containing Zn-free microparticles were cytocompatible and therefore appear most suitable for applications as an injectable biomaterial. This study proves the principle of creating bi- and tri-elemental microparticles to induce the gelation of GG to create injectable hydrogel-microparticle composites.

Loading Capacity versus Enzyme Activity in Anisotropic and Spherical Calcium Carbonate Microparticles.

A new method of fabrication of calcium carbonate microparticles of ellipsoidal, rhomboidal, and spherical geometries is reported by adjusting the relative concentration ratios of the initial salt solutions and/or the ethylene glycol content in the reaction medium. Morphology, porosity, crystallinity, and loading capacity of synthesized CaCO3 templates were characterized in detail. Particles harboring dextran or the enzyme guanylate kinase were obtained through encapsulation of these macromolecules using the layer-by-layer assembly technique to deposit positively and negatively charged polymers on these differently shaped CaCO3 templates and were characterized by confocal laser scanning fluorescence microscopy, fluorometric techniques, and enzyme activity measurements. The enzymatic activity, an important application of such porous particles and containers, has been analyzed in comparison with the loading capacity and geometry. Our results reveal that the particles' shape influences morphology of particles and that, as a result, affects the activity of the encapsulated enzymes, in addition to the earlier reported influence on cellular uptake. These particles are promising candidates for efficient drug delivery due to their relatively high loading capacity, biocompatibility, and easy fabrication and handling.