Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.This work is part of the ‘‘SpatioTemporal Omics Consortium’’ (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org. We would like to thank the MOTIC China Group, Rongqin Ke (Huaqiao University, Xiamen, China), Jiazuan Ni (Shenzhen University, Shenzhen, China), Wei Huang (Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), and Jonathan S. Weissman (Whitehead Institute, Boston, USA) for their help. This work was supported by the grant of Top Ten Foundamental Research Institutes of Shenzhen, the Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); Longqi Liu was supported by the National Natural Science Foundation of China (31900466) and Miguel A. Esteban’s laboratory at the Guangzhou Institutes of Biomedicine and Health by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), National Natural Science Foundation of China (92068106), and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075).S

Investigating second harmonic generation in collagen tissues

Collagen is the most abundant structural protein in the human body. When it is excited by femtosecond near infrared laser, second harmonic generation (SHG) signal at half the wavelength of the excitation wave is excited. For imaging thick tissues, the SHG signal is collected in the backward direction. The objective of this work is to elaborate the origin of the backward SHG in collagen at the fibril level and investigate some of its optic characteristics. The optic characteristics investigated include the wavelength dependence of SHG intensity, which is useful to analyze SHG in collagen tissues. However, the current published results are inconsistent. We study the microscopy system factors affecting the wavelength dependence and calibrate them by measuring the wavelength dependence of SHG intensity in a BaB₂O₄ crystal. With the proper calibration, typical wavelength dependence SHG spectra from mouse tail and Achilles tendon are investigated. The backward-collected SHG signal includes the backward generated SHG, and the forward generated but backward scattered SHG. Those two sources of the total backward SHG have different properties due to the difference in phase mismatch in the forward and backward directions. Here a non-invasive method is developed to separate them by using pinholes. By varying the pinhole size in a confocal multiphoton microscopy, the proportion of the backward scattered SHG to the total backward SHG can be obtained. Our results indicate that backward scattered SHG may not be the major source of backward SHG in the mouse tail tendon, which means significant SHG is purely generated in the backward direction. A large phase mismatch exists in generating backward SHG. Nevertheless, significant backward generated SHG has been observed in collagen tissues. We hypothesize that the periodic lattice structure of fibrillar collagen can provide a virtual momentum to assist the backward phase matching. Here the backward SHG phase matching is investigated in theory, simulation, and experiments, which are consistent and support the hypothesis. The various properties investigated in this thesis can provide a better understanding about SHG in collagen tissues and lead to new applications of SHG microscopy in diagnosing collagen related diseases in the future.Applied Science, Faculty ofElectrical and Computer Engineering, Department ofGraduat

Parametric wavelength exchange and its application in high speed optical signal processing

published_or_final_versionElectrical and Electronic EngineeringMasterMaster of Philosoph

Microporous Cyanate Resins: Synthesis, Porous Structure, and Correlations with Gas and Vapor Adsorptions

Three silicon and nitrogen-centered cyanate monomers tetrakis­(4-cyanatophenyl)­silane, tetrakis­(4-cyanatobiphenyl)­silane, and tris­(4-cyanatobiphenyl)­amine were designed and synthesized, which were then polymerized via thermal cyclotrimerization reaction to create highly porous cyanate resin networks with systematically varied nodes and linking struts. The chemical structures of monomers and polymers were confirmed by ¹H NMR, FTIR, solid-state ¹³C CP/MAS NMR spectra, and elemental analysis. The products are amorphous with 5% weight-loss temperatures over 428 °C. The results based on N₂ and CO₂ adsorption isotherms show that the pores in these polymers mainly locate in the microporous region, and the BET surface areas are up to 960 m² g^–1, which is the highest value for the porous cyanate resin reported to date. The nitrogen- and oxygen-rich characteristics of cyanate resins lead to the networks strong affinity for CO₂ and thereby high CO₂ adsorption capacity of 11.1 wt % at 273 K and 1.0 bar. The adsorption behaviors of H₂, CO₂, benzene, <i>n</i>-hexane, and water vapors were investigated by correlating with the chemical composition and porosity parameters of the networks as well as the physicochemical nature of adsorbates