Investigating the gene expression profiles of cells in seven embryonic stages with machine learning algorithms

The development of embryonic cells involves several continuous stages, and some genes are related to embryogenesis. To date, few studies have systematically investigated changes in gene expression profiles during mammalian embryogenesis. In this study, a computational analysis using machine learning algorithms was performed on the gene expression profiles of mouse embryonic cells at seven stages. First, the profiles were analyzed through a powerful Monte Carlo feature selection method for the generation of a feature list. Second, increment feature selection was applied on the list by incorporating two classification algorithms: support vector machine (SVM) and repeated incremental pruning to produce error reduction (RIPPER). Through SVM, we extracted several latent gene biomarkers, indicating the stages of embryonic cells, and constructed an optimal SVM classifier that produced a nearly perfect classification of embryonic cells. Furthermore, some interesting rules were accessed by the RIPPER algorithm, suggesting different expression patterns for different stages.     

Histomorphological study on embryogenesis of the honeybee Apis cerana

As important pollination species, honeybees play substantial impacts on the balance of global ecosystem, including two best-known honeybees Apis mellifera and Apis cerana. Embryogenesis is a fundamental stage of honeybee development and plays important roles in supporting the whole-life developmental process. However, few studies were reported on honeybee embryonic morphology using egg section, possibly due to the fragility of honeybee eggs and the difficulty of making embryonic sections. In this study, we reported a simply equipped method of frozen sectioning and PI (propidium iodide) staining to show the inner structure and cell distribution of A. cerena embryos at the different embryonic developmental stages. We found that the stages of A. cerena embryogenesis could also be typically classified into ten developmental stages, which are similar with the sister honeybee species, A. mellifera. To be noted, besides the cell distribution in the whole egg, we clearly observed the migration route of embryonic cells during the early embryonic development in A. cerena. This study provides a new insight into the whole process of honeybee embryogenesis from the perspective of egg sectioning, a histological basis for genetic manipulation using A. cerena eggs, and a reference method for egg sectioning for other insect species.     

Crucial stages of embryogenesis of <Emphasis Type="Italic">R. arvalis</Emphasis>: Part 1. Linear measurements of embryonic structures

Investigations of individual variability have allowed us to reveal the crucial (=nodal) stages in embryogenesis of the moor frog (Rana arvalis Nills.). These crucial stages are: the late gastrula stage (stages 18–20), the hatching stages (stages 32–33) and, apparently, early metamorphosis (stage 39). Moreover, we have found that each embryonic structure passes through its specific crucial stages. For example, stage 34 is crucial for the trait “tail width” but is internodal for all other embryonic traits. At this stage, larva passes from an attached to a free-swimming life style. We also found considerable differences between the different frog populations in the the level of developmental variability. These differences were associated with internodal developmental stages.     

Dynamic expression of Dab2 in the mouse embryonic central nervous system

Background  

Dab2, one of two mammalian orthologs of Drosophila Disabled, has been shown to be involved in cell positioning and formation of visceral endoderm during mouse embryogenesis, but its role in neuronal development is not yet fully understood. In this report, we have examined the localization of the Dab2 protein in the mouse embryonic central nervous system (CNS) at different developmental stages.     

Embryonic development of the pacific cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> (Gadidae)

Incubation of pacific cod eggs was divided into eight series, in which temperatures were set at −0.04°C to +4.03°C and warm and cold conditions alternated. The morphological changes that took place during the embryogenesis were described in detail using the results of the incubation. Twenty-two morphological characters that could be identified easily and that characterized the morphogenesis were defined in the course of development. The results of the incubation and data from the literature showed that the duration of the embryonic period in the Pacific cod’s lifecycle grew exponentially as water temperature decreased. It was found during the experiment that developing cod eggs survived low water temperatures up to freezing, as well as abrupt warming or cooling (over 3°C). According to the widely accepted Rass scale, the first stage of the Pacific cod embryogenesis takes 21% of its total duration, the second stage 23%, the third, 17%, and the fourth, 39%. However, at a temperature below 0°C, the relative duration of the stages of cleavage and embryonic shield was slightly shortened, whereas the mature embryo stage extended to almost half of the embryogenesis period. A more comprehensive analysis of temperature effects on embryogenesis revealed that the reduction of the rate of embryogenesis upon a temperature decrease occurred mostly at later stages of embryo growth. Modeling of development using defined morphological characters showed that the duration of embryogenesis grew linearly as the incubation temperature dropped in the first half of the embryogenesis and exponentially in the second half. A function was selected that described the obtained results most satisfactorily and that could be used for estimating the duration of the entire embryogenesis or any its stages within the range of water temperatures typical for Pacific cod.     

Development of polyembryonic insects: a major departure from typical insect embryogenesis

 The parasitic wasp Copidosoma floridanum represents the most extreme form of polyembryonic development known, forming up to 2000 embryos from a single egg. To understand the mechanisms of embryonic patterning in polyembryonic wasps and the evolutionary changes that led to this form of development we have analyzed embryonic development at the cellular level using confocal and scanning electron microscopy. C. floridanum embryogenesis can be divided into three phases: (1) early cleavage that leads to formation of a primary morula, (2) a proliferative phase that involves partitioning of embryonic cells into thousands of morulae, and (3) morphogenesis whereby individual embryos develop into larvae. This developmental program represents a major departure from typical insect embryogenesis, and we describe several features of morphogenesis unusual for insects. The early development of polyembryonic wasps, which likely evolved in association with a shift in life history to endoparasitism, shows several analogies with mammalian embryogenesis, including early separation of extraembryonic and embryonic cell lineages, formation of a morula and embryonic compaction. However, the late morphogenesis of polyembryonic wasps proceeds in a fashion conserved in all insects. Collectively, this suggests a lack of developmental constraints in early development, but a strong conservation of the phylotypic stage. Received: 27 June 1997 / Accepted: 11 January 1998     

Embryonic expression profile of phospholipid hydroperoxide glutathione peroxidase

The selenoenzyme phospholipid hydroperoxide glutathione peroxidase (PHGPx) is indispensable for murine embryonic development; yet, the cellular mechanisms leading to embryonic death around gastrulation are still unclear. To investigate PHGPx expression patterns during embryogenesis, we performed a detailed analysis that revealed a complex expression profile. Up to embryonic day 9.5, PHGPx was ubiquitously expressed, which was, albeit to a lower extent, maintained throughout later stages of embryogenesis. Notably, strong expression was frequently observed in epithelial tissue. A transient increase in PHGPx expression was detected in developing tissues, suggesting a crucial role for PHGPx in proliferation and differentiation. By semi-quantitative RT-PCR analysis we observed that the cytosolic form of PHGPx was present in embryonic and somatic tissues whereas the mitochondrial and nuclear forms were detectable only in testicular tissue. This strongly suggests that it is the cytosolic form of PHGPx that is indispensable for embryonic development.     

Somatic embryogenesis versus zygotic embryogenesis in Ensete superbum

In vitro regenerated corm with a shoot incubated on MS medium with modified combination of vitamins supplemented with 2 mg l^–1 2,4-D, 1.5 mg l^–1 BA and 1000 mg l^–1 L-glutamine formed an embryogenic callus. On transfer to a hormone free medium the callus turned black and formed whitish spherical nodules on the peripheral region from which mature embryos grew out in about 40 days. Histological preparations at successive stages in development confirmed the origin of somatic embryos initiated from single cells of the callus. Detailed analysis of the ontogeny of the somatic embryogenesis and zygotic embryogenesis has been done in the present study. Comparison of the ontogenetic stages of the somatic embryogenesis to that of zygotic embryogenesis has shown that the early segmentation of the embryo, the organization of the embryonic apex, formation of cotyledon and epicotyl, the morphology and shape of the zygotic and somatic embryos of E. superbum at successive stages show remarkable similarities in spite of the different environments in which they have developed and differen-tiated.     

华山松胚性愈伤组织诱导与幼胚离体培养

探索华山松(Pinus armandii)体细胞胚胎发生技术对其实施规模化无性繁殖和开展遗传转化具有重要意义。本文以1/2LM为基本培养基, 通过激素调节等措施对华山松的胚性愈伤组织诱导和幼胚的离体培养技术进行了初步研究。研究结果: 胚性愈伤组织诱导率最高可达52.71%, 但愈伤组织继代培养后没有体细胞胚胎的分化; 首次从其子叶期的幼胚中直接诱导出具有根和茎的完整植株, 诱导率达92%以上。文章确认了采集的幼胚发育状态对胚性愈伤组织的诱导有重要影响, 并对诱导的培养条件等进行了探讨。     

华山松胚性愈伤组织诱导与幼胚离体培养

探索华山松（Pinus armandii）体细胞胚胎发生技术对其实施规模化无性繁殖和开展遗传转化具有重要意义。本文以1／2LM为基本培养基,通过激素调节等措施对华山松的胚性愈伤组织诱导和幼胚的离体培养技术进行了初步研究。研究结果：胚性愈伤组织诱导率最高可达52．71％,但愈伤组织继代培养后没有体细胞胚胎的分化;首次从其子叶期的幼胚中直接诱导出具有根和茎的完整植株,诱导率达92％以上。文章确认了采集的幼胚发育状态对胚性愈伤组织的诱导有重要影响,并对诱导的培养条件等进行了探讨。     

Fine-tuning of fgf8a expression through alternative polyadenylation has a selective impact on Fgf-associated developmental processes

The formation of distinct 3′UTRs through alternative polyadenylation is a mechanism of gene expression regulation that has been implicated in many physiological and pathological processes. However, its functions in the context of vertebrate embryonic development have been largely unaddressed, in particular with a gene-specific focus. Here we show that the most abundant 3′UTR for the zebrafish fgf8a gene in the developing embryo mediates a strong translational repression, when compared to a more sparsely used alternative 3′UTR, which supports a higher translation efficiency. By inducing a shift in the selection efficiency of the associated polyadenylation sites, we show a temporally and spatially specific impact of fgf8a 3′UTR usage on embryogenesis, in particular at late stages during sensory system development. In addition, we identified a previously undescribed role for Fgf signalling in the initial stages of superficial retinal vascularization. These results reveal a critical functional importance of gene-specific alternative 3′UTRs in vertebrate embryonic development.     

3110009F21Rik基因在小鼠胚胎发育中的表达研究

目的:探讨小鼠胚胎发育过程中3110009F21Rik基因的时空特异性表达模式,为后续功能研究奠定基础。方法:对E15.5小鼠胚胎脑组织进行印记分析,检测基因的印记表达状态;应用全胚胎和组织原位杂交技术检测3110009F21Rik基因在E9.5~E15.5小鼠胚胎中的特异性时空表达模式。结果:印记分析显示3110009F21Rik基因在E15.5脑组织中为父母本等位基因双表达;原位杂交结果显示3110009F21Rik基因在E9.5~E15.5脑组织中持续表达,在E9.5~E11.5主要脏器中未检测到,但自E12.5开始在主要脏器中持续表达,随着发育进程进行,目的基因在胚胎骨骼中的相对表达水平逐步升高,至E15.5阶段大部分骨骼中都检测到目的基因表达。结论:3110009F21Rik基因在脑组织中的持续表达和表达模式的动态变化提示其可能参与胚胎发育过程中大脑神经网络的构建,其在软骨原基和软骨中的相对表达逐渐增强表明其可能参与了小鼠胚胎过程中骨的发育和形成及软骨分化。