Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development.

Development of multicellular organisms is orchestrated by persistent cell-cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single-cell RNA-seq technology cannot adequately analyze cell-cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell-cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single-cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells upregulate Lhx5 and Nkx2-1 genes, when exclusively interacting with definitive endoderm (DE) cells. Moreover, there was a reciprocal impact on the transcriptome of DE cells, as they tend to upregulate Rax and Gsc when in contact with NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-t-distributed stochastic neighboring embedding to display the pseudospatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis.

Altitude is correlated with body size differences among Cotesia flavipes (Hymenoptera: Braconidae) wasps collected in two mountain ranges.

Living at high altitudes impose physiological and ecological challenges to which species may respond altering their body size, body proportions, and the shape of their body parts. Despite the importance of this topic for understanding the origin of species diversity, little attention has been invested in this phenomenon at the populational level. This paper study the relationship between altitude and body size, body proportions, and forewing shape venation of two populations of the parasitoid wasp Cotesia flavipes. Wasps were collected from Diatraea spp. larvae from sugarcane crops in two Colombian mountain ranges that cover between 600 m and 2143 m of altitude. Linear measurements of different body regions and geometric morphometrics of the forewing were subject to multivariate comparisons and allometric analyses to assess variation and to compare trends between ranges. Central (600 m to 1704 m) and Eastern Cordillera (877 m to 2143 m) populations showed different trends between body size and altitude. Allometric trends were not uniform within or between populations nor between structures. The allometric slopes of five body measurements from a single altitude differed from these from its own mountain range suggesting that body size trends along the cordilleras are a consequence of altitude and not of intrinsic body resource allocation processes. Wing shape between populations differed; however, these changes were poorly related to altitude. In agreement with recent studies in other groups, the observed allometric and wing shape differences between the two C. flavipes populations could be a plasticity response to altitude with interesting implications for posterior genetic differentiation.