Analysis of enterovirus infection is difficult in animals because they express different virus receptors than humans, and static cell culture systems do not reproduce the physical complexity of the ...human intestinal epithelium. Here, using coxsackievirus B1 (CVB1) as a prototype enterovirus strain, we demonstrate that human enterovirus infection, replication and infectious virus production can be analyzed in vitro in a human Gut-on-a-Chip microfluidic device that supports culture of highly differentiated human villus intestinal epithelium under conditions of fluid flow and peristalsis-like motions. When CVB1 was introduced into the epithelium-lined intestinal lumen of the device, virions entered the epithelium, replicated inside the cells producing detectable cytopathic effects (CPEs), and both infectious virions and inflammatory cytokines were released in a polarized manner from the cell apex, as they could be detected in the effluent from the epithelial microchannel. When the virus was introduced via a basal route of infection (by inoculating virus into fluid flowing through a parallel lower 'vascular' channel separated from the epithelial channel by a porous membrane), significantly lower viral titers, decreased CPEs, and delayed caspase-3 activation were observed; however, cytokines continued to be secreted apically. The presence of continuous fluid flow through the epithelial lumen also resulted in production of a gradient of CPEs consistent with the flow direction. Thus, the human Gut-on-a-Chip may provide a suitable in vitro model for enteric virus infection and for investigating mechanisms of enterovirus pathogenesis.
RNA-sequencing (RNA-seq) measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. In contrast, in situ hybridization provides the location of ...gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq, our method enriches for context-specific transcripts over housekeeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d.
Spontaneous Raman spectroscopy is a powerful characterization tool for graphene research. Its extension to the coherent regime, despite the large nonlinear third-order susceptibility of graphene, has ...so far proven challenging. Due to its gapless nature, several interfering electronic and phononic transitions concur to generate its optical response, preventing to retrieve spectral profiles analogous to those of spontaneous Raman. Here we report stimulated Raman spectroscopy of the G-phonon in single and multi-layer graphene, through coherent anti-Stokes Raman Scattering. The nonlinear signal is dominated by a vibrationally non-resonant background, obscuring the Raman lineshape. We demonstrate that the vibrationally resonant coherent anti-Stokes Raman Scattering peak can be measured by reducing the temporal overlap of the laser excitation pulses, suppressing the vibrationally non-resonant background. We model the spectra, taking into account the electronically resonant nature of both. We show how coherent anti-Stokes Raman Scattering can be used for graphene imaging with vibrational sensitivity.
Highly Multiplexed Subcellular RNA Sequencing in Situ Lee, Je Hyuk; Daugharthy, Evan R.; Scheiman, Jonathan ...
Science (American Association for the Advancement of Science),
03/2014, Letnik:
343, Številka:
6177
Journal Article
Recenzirano
Odprti dostop
Understanding the spatial organization of gene expression with single-nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here, we describe ...fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked complementary DNA (cDNA) amplicons are sequenced within a biological sample. Using 30-base reads from 8102 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.
Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates; however, the regulatory circuits specifying these states and enabling transitions between them are not ...well understood. Here we set out to characterize transcriptional heterogeneity in mouse PSCs by single-cell expression profiling under different chemical and genetic perturbations. Signalling factors and developmental regulators show highly variable expression, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signalling pathways and chromatin regulators. Notably, either removal of mature microRNAs or pharmacological blockage of signalling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency network, enhanced self-renewal and a distinct chromatin state, an effect mediated by opposing microRNA families acting on the Myc/Lin28/let-7 axis. These data provide insight into the nature of transcriptional heterogeneity in PSCs.
The equilibrium optical phonons of graphene are well characterized in terms of anharmonicity and electron-phonon interactions; however, their non-equilibrium properties in the presence of hot charge ...carriers are still not fully explored. Here we study the Raman spectrum of graphene under ultrafast laser excitation with 3 ps pulses, which trade off between impulsive stimulation and spectral resolution. We localize energy into hot carriers, generating non-equilibrium temperatures in the ~1700-3100 K range, far exceeding that of the phonon bath, while simultaneously detecting the Raman response. The linewidths of both G and 2D peaks show an increase as function of the electronic temperature. We explain this as a result of the Dirac cones' broadening and electron-phonon scattering in the highly excited transient regime, important for the emerging field of graphene-based photonics and optoelectronics.
Abstract Background The pathogenesis of nonalcoholic fatty liver disease (NAFLD) has been attributed to increased systemic inflammation and insulin resistance mediated by visceral adipose tissue ...(VAT), although the exact mechanisms are undefined. Exosomes are membrane-derived vesicles containing messenger RNA, microRNA, and proteins, which have been implicated in cancer, neurodegenerative, and autoimmune diseases, which we postulated may be involved in obesity-related diseases. We isolated exosomes from VAT, characterized their content, and identified their potential targets. Targets included the transforming growth factor beta (TGF-β) pathway, which has been linked to NAFLD. We hypothesized that adipocyte exosomes would integrate into HepG2 and hepatic stellate cell lines and cause dysregulation of the TGF-β pathway. Methods Exosomes from VAT from obese and lean patients were isolated and fluorescently labeled, then applied to cultured hepatic cell lines. After incubation, culture slides were imaged to detect exosome uptake. In separate experiments, exosomes were applied to cultured cells and incubated 48-h. Gene expression of TGF-β pathway mediators was analyzed by polymerase chain reaction, and compared with cells, which were not exposed to exosomes. Results Fluorescent-labeled exosomes integrated into both cell types and deposited in a perinuclear distribution. Exosome exposure caused increased tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) and integrin ανβ-5 expression and decreased matrix metalloproteinase-7 and plasminogen activator inhibitor-1 expression in to HepG2 cells and increased expression of TIMP-1, TIMP-4, Smad-3, integrins ανβ-5 and ανβ-8, and matrix metalloproteinase-9 in hepatic stellate cells. Conclusions Exosomes from VAT integrate into liver cells and induce dysregulation of TGF-β pathway members in vitro and offers an intriguing possibility for the pathogenesis of NAFLD.
Manipulating the macroscopic phases of solids using ultrashort light pulses has resulted in spectacular phenomena, including metal-insulator transitions, superconductivity and subpicosecond ...modification of magnetic order. The development of this research area strongly depends on the understanding and optical control of fundamental interactions in condensed matter, in particular the exchange interaction. However, disentangling the timescales relevant for the contributions of the exchange interaction and spin dynamics to the exchange energy, Eex , is a challenge. Here, we introduce femtosecond stimulated Raman scattering to unravel the ultrafast photo-induced dynamics of magnetic excitations at the edge of the Brillouin zone. We find that femtosecond laser excitation of the antiferromagnet KNiF3 triggers a spectral shift of the two-magnon line, the energy of which is proportional to Eex . By unravelling the photo-induced modification of the two-magnon line frequency from a dominating nonlinear optical effect, we find that Eex is increased by the electromagnetic stimulus.
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