Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice.

The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding a genome's structure-function relationship, yet this is challenging for existing methods. Here we present 'Linking mRNA to Chromatin Architecture (LiMCA)', which jointly profiles the 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we successfully characterized chromatin accessibility, as well as paired 3D genome structures and gene expression information, of individual developing olfactory sensory neurons. We expanded the repertoire of known olfactory receptor (OR) enhancers and discovered unexpected rules of their dynamics: OR genes and their enhancers are most accessible during early differentiation. Furthermore, we revealed the dynamic spatial relationship between ORs and enhancers behind stepwise OR expression. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the 'one neuron-one receptor' selection process.

Simultaneous two-color stimulated Raman scattering microscopy by adding a fiber amplifier to a 2 ps OPO-based SRS microscope.

Stimulated Raman scattering (SRS) microscopy is a label-free chemical imaging technique. Two-color imaging is often necessary to determine the distribution of chemical species in SRS microscopy. Current multi-color SRS imaging methods involve complicated instrumentation or longer data acquisition time or are limited to transmission imaging. In this Letter, we show that by adding a simple fiber amplifier to a 2 ps laser source and optical-parametric-oscillator-based SRS setup, one can achieve simultaneous two-color or frequency modulation SRS microscopy. The fiber amplifier can generate a wavelength tunable laser of ±10 nm around the Stokes laser wavelength at 1031 nm with average power greater than 200 mW. In vivo and ex vivo lipid-protein imaging of mouse brain and skin is demonstrated. To further demonstrate the potential of this technique in high-speed in vivo imaging, white blood cells in a blood stream are imaged in a live mouse.

Improving the accuracy of brain tumor surgery via Raman-based technology.

Despite advances in the surgical management of brain tumors, achieving optimal surgical results and identification of tumor remains a challenge. Raman spectroscopy, a laser-based technique that can be used to nondestructively differentiate molecules based on the inelastic scattering of light, is being applied toward improving the accuracy of brain tumor surgery. Here, the authors systematically review the application of Raman spectroscopy for guidance during brain tumor surgery. Raman spectroscopy can differentiate normal brain from necrotic and vital glioma tissue in human specimens based on chemical differences, and has recently been shown to differentiate tumor-infiltrated tissues from noninfiltrated tissues during surgery. Raman spectroscopy also forms the basis for coherent Raman scattering (CRS) microscopy, a technique that amplifies spontaneous Raman signals by 10,000-fold, enabling real-time histological imaging without the need for tissue processing, sectioning, or staining. The authors review the relevant basic and translational studies on CRS microscopy as a means of providing real-time intraoperative guidance. Recent studies have demonstrated how CRS can be used to differentiate tumor-infiltrated tissues from noninfiltrated tissues and that it has excellent agreement with traditional histology. Under simulated operative conditions, CRS has been shown to identify tumor margins that would be undetectable using standard bright-field microscopy. In addition, CRS microscopy has been shown to detect tumor in human surgical specimens with near-perfect agreement to standard H & E microscopy. The authors suggest that as the intraoperative application and instrumentation for Raman spectroscopy and imaging matures, it will become an essential component in the neurosurgical armamentarium for identifying residual tumor and improving the surgical management of brain tumors.

Fiber four-wave mixing source for coherent anti-Stokes Raman scattering microscopy.

We present a fiber-format picosecond light source for coherent anti-Stokes Raman scattering microscopy. Pulses from a Yb-doped fiber amplifier are frequency converted by four-wave mixing (FWM) in normal-dispersion photonic crystal fiber to produce a synchronized two-color picosecond pulse train. We show that seeding the FWM process overcomes the deleterious effects of group-velocity mismatch and allows efficient conversion into narrow frequency bands. The source generates more than 160 mW of nearly transform-limited pulses tunable from 775 to 815 nm. High-quality coherent Raman images of animal tissues and cells acquired with this source are presented.

Broadly tunable dual-wavelength light source for coherent anti-Stokes Raman scattering microscopy.

The signal and idler beams from a picosecond, synchronously pumped optical parametric oscillator (OPO) provide the two colors necessary for coherent anti-Stokes Raman scattering (CARS) microscopy. The OPO provides a continuously tunable frequency difference between the two beams over a broad range of Raman shifts (100-3700 cm(-1)) by varying the temperature of a single nonlinear crystal. The near-infrared output (900-1300 nm) allows for deep penetration into thick samples and reduced nonlinear photodamage. Applications of this light source to in vivo cell and ex vivo tissue imaging are demonstrated.