Cindy Liu

Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. We developed and applied a technology for 3D intact-tissue RNA sequencing, termed STARmap (spatially-resolved transcript amplicon readout mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy, and reproducibility. Moving to thick tissue blocks, we observed a molecularly defined gradient distribution of excitatory-neuron subtypes across cubic millimeter-scale volumes (>30,000 cells) and a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.

Microbial communities are complex and dynamic systems that are primarily structured according to their members' ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.

Analysis of muscle architecture, traditionally conducted via gross dissection, has been used to evaluate adaptive relationships between anatomical form and behavioral function. However, gross dissection cannot preserve three-dimensional relationships between myological structures for analysis. To analyze such data, we employ diffusible, iodine-based contrast-enhanced computed tomography (DiceCT) to explore the relationships between feeding ecology and masticatory muscle microanatomy in eight dietarily diverse strepsirrhines: allowing, for the first time, preservation of three-dimensional fascicle orientation and tortuosity across a functional comparative sample. We find that fascicle properties derived from these digital analyses generally agree with those measured from gross-dissected conspecifics. Physiological cross-sectional area was greatest in species with mechanically challenging diets. Frugivorous taxa and the wood-gouging species all exhibit long jaw adductor fascicles, while more folivorous species show the shortest relative jaw adductor fascicle lengths. Fascicle orientation in the parasagittal plane also seems to have a clear dietary association: most folivorous taxa have masseter and temporalis muscle vectors that intersect acutely while these vectors intersect obliquely in more frugivorous species. Finally, we observed notably greater magnitudes of fascicle tortuosity, as well as greater interspecific variation in tortuosity, within the jaw adductor musculature than in the jaw abductors. While the use of a single specimen per species precludes analysis of intraspecific variation, our data highlight the diversity of microanatomical variation that exists within the strepsirrhine feeding system and suggest that muscle architectural configurations are evolutionarily labile in response to dietary ecology-an observation to be explored across larger samples in the future.