Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential, but widely used animal models exhibit limitations. Here we present a modular, microfluidics-based model (HuMiX, human–microbial crosstalk), which allows co-culture of human and microbial cells under conditions representative of the gastrointestinal human–microbe interface. We demonstrate the ability of HuMiX to recapitulate in vivo transcriptional, metabolic and immunological responses in human intestinal epithelial cells following their co-culture with the commensal Lactobacillus rhamnosus GG (LGG) grown under anaerobic conditions. In addition, we show that the co-culture of human epithelial cells with the obligate anaerobe Bacteroides caccae and LGG results in a transcriptional response, which is distinct from that of a co-culture solely comprising LGG. HuMiX facilitates investigations of host–microbe molecular interactions and provides insights into a range of fundamental research questions linking the gastrointestinal microbiome to human health and disease.

Interferometric near-field optical microscopy achieving a resolution of 10 angstroms is demonstrated. The scattered electric field variation caused by a vibrating probe tip in close proximity to a sample surface is measured by encoding it as a modulation in the optical phase of one arm of an interferometer. Unlike in regular near-field optical microscopes, where the contrast results from a weak source (or aperture) dipole interacting with the polarizability of the sample, the present form of imaging relies on a fundamentally different contrast mechanism: sensing the dipole-dipole coupling of two externally driven dipoles (the tip and sample dipoles) as their spacing is modulated.

We demonstrate a new method whereby near-field optical microscope resolution can be extended to the nanometer regime. The technique is based on measuring the modulation of the scattered electric field from the end of a sharp silicon tip as it is stabilized and scanned in close proximity to a sample surface. Our initial results demonstrate resolution in the 3 nm range--comparable to what can be achieved with typical attractive mode atomic force microscopes. Theoretical considerations predict that the ultimate resolution achievable with this approach could be close to the atomic level.Following the demonstration of super-resolution by nearfield scarming microscopy at microwave frequencies' and its subsequent extension to the visible regionz9 the field of near-field scanning microscopy (NSOM) has attracted much attention. Particularly over the past few years, NSOM has enjoyed a rapid growth."15 This growth has been assisted by several important contributions to the technology such as the use of tapered single mode optical fibers," independently stabilizing the tip-sample spacing by shear-force contro17'8 and methods for measuring the polarization9 and fluorescence" of samples on the sub-50 nm scale. In this letter, we introduce a technique whereby the resolution of near-field optical microscopes can be extended below 1 nm, i.e., over an order of magnitude better than what has been achieved so far.The majority of near-field optical microscopes employ tapered single mode optical fibers coated on the sides with aluminum in order to form a subwavelength aperture at their ends. The aluminum (skin depth 12 nm at 633 nm wavelength) which is essential for the operation of most NSOMs serves to confine the light within the optical fiber as it enters the tip end thereby defining either a tiny light source (for illumination mode NSOM) or a tiny light collector (for collection mode NSOM). The smallest aperture that can be made in this way cannot be much smaller than twice the optical skin depth in aluminum, since the light has to be significantly attenuated as it leaks out of the fiber sides into the aluminum in order to define an aperture. Thus, spatial resolutions achieved in the NSOM are in the 30-50 nm range. This resolution although superior to the early images taken with NSOM are still an order of magnitude away from what can be achieved with typical attractive mode atomic force microscopes (AFMs>.~~ The concept we have explored is based on an idea that occurred to one of us several years ag0.t' Rather than transmitting light through a fine aperture, we use the spherical light scattering from a tip end of a standard Al?M or scanning tunnel microscopy @TM) to define the light source. Although in principle this concept allows one tomake scattering sources down to atomic dimensions (as in STM and AFM tips), it provides significant challenges for detecting the minute quantity of scattered light from the tip end in the presence of a large background. We have been able to overcome these difficulties. Here we present initial resu...

DNA on mica can be imaged in the atomic force microscope (AFM) in water or in some buffers if the sample has first been dehydrated thoroughly with propanol or by baking in vacuum and if the sample is imaged with a tip that has been deposited in the scanning electron microscope (SEM). Without adequate dehydration or with an unmodified tip, the DNA is scraped off the substrate by AFM-imaging in aqueous solutions. The measured heights and widths of DNA are larger in aqueous solutions than in propanol. The measured lengths of DNA molecules are the same in propanol and in aqueous solutions and correspond to the base spacing for B-DNA, the hydrated form of DNA; when the DNA is again imaged in propanol after buffer, however, it shortens to the length expected for dehydrated A-DNA. Other results include the imaging of E. coli RNA polymerase bound to DNA in a propanol-water mixture and the observation that washing samples in the AFM is an effective way of disaggregating salt-DNA complexes. The ability to image DNA in aqueous solutions has potential applications for observing processes involving DNA in the AFM.

Rapid biodosimetry tools are required to assist with triage in the case of a large-scale radiation incident. Here, we aimed to determine the dose-assessment accuracy of the well-established dicentric chromosome assay (DCA) and cytokinesis-block micronucleus assay (CBMN) in comparison to the emerging γ-H2AX foci and gene expression assays for triage mode biodosimetry and radiation injury assessment. Coded blood samples exposed to 10 X-ray doses (240 kVp, 1 Gy/min) of up to 6.4 Gy were sent to participants for dose estimation. Report times were documented for each laboratory and assay. The mean absolute difference (MAD) of estimated doses relative to the true doses was calculated. We also merged doses into binary dose categories of clinical relevance and examined accuracy, sensitivity and specificity of the assays. Dose estimates were reported by the first laboratories within 0.3–0.4 days of receipt of samples for the γ-H2AX and gene expression assays compared to 2.4 and 4 days for the DCA and CBMN assays, respectively. Irrespective of the assay we found a 2.5–4-fold variation of interlaboratory accuracy per assay and lowest MAD values for the DCA assay (0.16 Gy) followed by CBMN (0.34 Gy), gene expression (0.34 Gy) and γ-H2AX (0.45 Gy) foci assay. Binary categories of dose estimates could be discriminated with equal efficiency for all assays, but at doses ≥1.5 Gy a 10% decrease in efficiency was observed for the foci assay, which was still comparable to the CBMN assay. In conclusion, the DCA has been confirmed as the gold standard biodosimetry method, but in situations where speed and throughput are more important than ultimate accuracy, the emerging rapid molecular assays have the potential to become useful triage tools.