Characterization and expression pattern of two zebrafishatf7 genes

Neurulation in the posterior region of zebrafish, Danio rerio embryos

The neural tube of amniotes is formed through different mechanisms that take place in the anterior and posterior regions and involve neural plate folding or mesenchymal condensation followed by its cavitation. Meanwhile, in teleost trunk region, the neural plate forms the neural keel, while the lumen develops later. However, the data on neurulation and other morphogenetic processes in the posterior body region in Teleostei remain fragmentary. We proposed that there could be variations in the morphogenetic processes, such as cell shape changes and cell rearrangements, in the posterior region compared to the anterior one at the different stages. Here, we performed morphological and histochemical analyses of morphogenetic processes with an emphasis on neurulation in the zebrafish tail bud (TB) and posterior region. To analyze the posterior expression of sox2 and tbxta we performed whole mount in situ hybridization. We showed that the TB cells of variable shapes and orientation are tightly packed, and the neural and notochord primordia develop first. The shape of the neural primordium undergoes numerous changes as a result of cell rearrangements leading to the development of the neural rod. At the prim-6 stage, the cells of the neural primordium directly form the neural rod. The neuroepithelial cells undergo sequential shape changes. At the stage of the neural rod formation, the apical regions of triangular neuroepithelial cells of the floor plate are enriched in F-actin. The neurocoel development onset is above the apical poles of neuroepithelial cells. The expression domains of sox2 and tbxta become more restricted during the development.

Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts

Replicative senescence is of fundamental importance for the process of cellular aging, since it is a property of most of our somatic cells. Here, we elucidated this process by comparing gene expression changes, measured by RNA-seq, in fibroblasts originating from two different tissues, embryonic lung (MRC-5) and foreskin (HFF), at five different time points during their transition into senescence. Although the expression patterns of both fibroblast cell lines can be clearly distinguished, the similar differential expression of an ensemble of genes was found to correlate well with their transition into senescence, with only a minority of genes being cell line specific. Clustering-based approaches further revealed common signatures between the cell lines. Investigation of the mRNA expression levels at various time points during the lifespan of either of the fibroblasts resulted in a number of monotonically up- and downregulated genes which clearly showed a novel strong link to aging and senescence related processes which might be functional. In terms of expression profiles of differentially expressed genes with age, common genes identified here have the potential to rule the transition into senescence of embryonic lung and foreskin fibroblasts irrespective of their different cellular origin.

Functional divergence of gene duplicates - a domain-centric view

Background

Gene duplicates have been shown to evolve at different rates. Here we further investigate the mechanism and functional underpinning of this phenomenon by assessing asymmetric evolution specifically within functional domains of gene duplicates.

Results

Based on duplicate genes in five teleost fishes resulting from a whole genome duplication event, we first show that a Fisher Exact test based approach to detect asymmetry is more sensitive than the previously used Likelihood Ratio test. Using our Fisher Exact test, we found that the evolutionary rate asymmetry in the overall protein is largely explained by the asymmetric evolution within specific protein domains. Moreover, among cases of asymmetrically evolving domains, for the gene copy containing a fast evolving domain, the non-synonymous substitutions often cluster within the fast evolving domain. We found that rare substitutions were preferred within asymmetrically evolving domains suggestive of functional divergence. While overall ~32 % of the domains tested were found to be evolving asymmetrically, certain protein domains such as the Tyrosine and Ser/Thr Kinase domains had a much greater prevalence of asymmetric evolution. Finally, based on the spatial expression of Zebra fish duplicate proteins during development, we found that protein pairs containing asymmetrically evolving domains had a greater divergence in gene expression as compared to the duplicate proteins that did not exhibit asymmetric evolution.

Conclusions

Taken together, our results suggest that the previously observed asymmetry in the overall duplicate protein evolution is largely due to divergence of specific domains of the protein, and coincides with divergence in spatial expression domains.