The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information

Abstract

Background: Embryos of taxonomically different vertebrates are thought to pass through a stage in which they resemble one another morphologically. This "vertebrate phylotypic stage" may represent the basic vertebrate body plan that was established in the common ancestor of vertebrates. However, much controversy remains about when the phylotypic stage appears, and whether it even exists. To overcome the limitations of studies based on morphological comparison, we explored a comprehensive quantitative method for defining the constrained stage using expressed sequence tag (EST) data, gene ontologies (GO), and available genomes of various animals. If strong developmental constraints occur during the phylotypic stage of vertebrate embryos, then genes conserved among vertebrates would be highly expressed at this stage.

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

“…While some studies suggest that low doses (<500 Gray) of radiation have only negligible effect on insects survivorship, the long‐term effects of X‐rays on insects have remained poorly studied so far (Socha, Westneat, Harrison, Waters, & Lee, 2007; Westneat, Socha, & Lee, 2008). …”

“…In order to include the X‐ray CT analysis in vivo in ecological research, it is crucial to understand the effects of the radiation on the organisms before biological interpretation (Socha et al., 2007). In addition to the radiation, there are several steps of specimen preparation (such as staining and anesthesia) than can be potentially harmful.…”

“…In addition to the radiation, there are several steps of specimen preparation (such as staining and anesthesia) than can be potentially harmful. In some studies, tissue differentiation was achieved by staining live animals through dietary supplementation (e.g., with cadmium tungstate (CdWO 4 ) and iodine) (Kim, Seo, Lim, & Lee, 2012; Socha et al., 2007), or injecting compounds into the circulatory system (Greco, Tong, Soleimani, Bell, & Schäfer, 2012). There are few studies about long‐term effects of X‐rays doses in invertebrates, and Kanao, Okamoto, Miyachi, and Nohara (2003) showed that low doses (0.5 Grays) caused transgenerational changes of emergence patterns in Drosophila melanogaster and this area would clearly need further study.…”

“…1 cm) can take several weeks (Friedrich & Beutel, 2008; Socha et al., 2007). In this review, we focus on the preparation of ex vivo specimens.…”

“…As pointed out before in several reviews (Metscher, 2013; Socha et al., 2007; Westneat et al., 2008), X‐ray CT bears the potential to generate valuable morphological data from specimens and structures that would be impossible or expensive to acquire using other approaches (e.g., synchrotron or MRI facilities) (Brinkmann et al., 2016) or that would be time‐consuming (e.g., microtomy). Although reconstruction artifacts will inevitably be present in some images (Davis & Elliott, 2006), in this review we present several successful applications of this technique—and its variations—in ecological studies (Appendix S1).…”