Complete cDNAs for CDC42 from chicken cochlea and mouse liver

Identification of hub genes involved in apparent metabolizable energy of chickens

Feed efficiency is one of the most economically significant traits in a breeding program. Apparent metabolizable energy is the most used method to evaluate energy utilization for feed efficiency. The purpose of this study was to identify candidate genes of chickens with divergent apparent metabolizable energy by bioinformatics analysis. The gene expression profile of duodenal of the highest and lowest apparent metabolizable energy-ranked birds were analyzed. Differentially expressed genes were picked out using GEO2R tool. Gene ontology and pathway analysis were performed using bioinformatics tools. Cytoscape software was used to visualize protein-protein network. There were 201 DEGs, including 99 up-regulated genes enriched in metabolic pathways, Cellular senescence and Focal adhesion, and 102 down-regulated genes enriched in metabolic pathways, Regulation of actin cytoskeleton, Neuroactive ligand-receptor interaction, Calcium signaling pathway and Focal adhesion. Two important modules were detected and pathway enrichment analysis showed that they were mainly associated with Focal adhesion, Regulation of actin cytoskeleton and RNA transport. Fifteen hub genes were selected and among them, ITGA8, CDC42 and GSK3B might be the core genes related to apparent metabolizable energy of chickens. These hub genes can be used as biomarkers for apparent metabolizable energy and feed efficiency in breeding program of chickens.

Toxicogenomic effects of neonatal exposure to diethylstilbestrol on mouse testicular gene expression in the long term: a study using cDNA microarray analysis

We examined the effect of neonatal exposure to diethylstilbestrol (DES) on mouse testicular gene expression, using in-house mouse fetus (day 14.5) cDNA microarrays. Newborn male ICR mice were exposed to DES (50 microg/mouse/day) from neonatal day 1 to 5. Differential expression was detected in 14 genes in 4-week-old (day 28) mouse testes by cDNA microarray analysis; 11 genes (AI035263, AU080565, AU080361, AU080678, AI131681, AU080631, AA986882, AI037066, AA986537, AI156816, and AI596237) were up-regulated and three genes (AI131656, AI118968, and AI117606) were down-regulated in DES-treated mouse testes. Higher expression levels of the former eight genes, out of the up-regulated genes picked-up by the microarray, were also confirmed by reverse transcription and real-time polymerase chain reaction (real-time RT-PCR) analysis. However, the differential expression of other genes could not be confirmed. Real-time RT-PCR analysis also revealed that expression levels of the eight genes were still higher in DES-treated testes at 8 and 12 weeks of age. Our results suggest that cDNA microarray analysis is a useful method by which a large number of gene expressions are simultaneously detected and changes in gene expression are screened. In addition, our results suggest that these genes, whose expressions are changed in the testes of adult mice by fetal or neonatal exposure to exogenous chemicals, might be candidates for predictive biological markers.

Differential display and gene arrays to examine auditory plasticity

Differential gene expression forms the basis for development, differentiation, regeneration, and plasticity of tissues and organs. We describe two methods to identify differentially expressed genes. Differential display, a PCR-based approach, compares the expression of subsets of genes under two or more conditions. Gene arrays, or DNA microarrays, contain cDNAs from both known genes and novel genes spotted on a solid support (nylon membranes or glass slides). Hybridization of the arrays with RNA isolated from two different experimental conditions allows the simultaneous analysis of large numbers of genes, from hundreds to thousands to whole genomes. Using differential display to examine differential gene expression after noise trauma in the chick basilar papilla, we identified the UBE3B gene that encodes a new member of the E3 ubiquitin ligase family (UBE3B). UBE3B is highly expressed immediately after noise in the lesion, but not in the undamaged ends, of the chick basilar papilla. UBE3B is most similar to a ubiquitin ligase gene from Caenorhabditis elegans, suggesting that this gene has been conserved throughout evolution. We also describe preliminary experiments to profile gene expression in the cochlea and brain with commercially available low density gene arrays on nylon membranes and discuss potential applications of this and DNA microarray technology to the auditory system.

Differential expression of the small GTP-binding proteins RhoA, RhoB, Cdc42u and Cdc42b in developing rat neocortex

Studies with cultured cells indicate that small GTPases of the Rho family may be involved in cell proliferation, differentiation, as well as migration. Therefore, we have studied the expression of four members of this protein family, i.e., RhoA, RhoB, the ubiquitous Cdc42u, and brain specific Cdc42b, during the embryonic and early postnatal development of rat neocortex. A clear isoform specificity of expression was found during the prenatal development. Thus, RhoA and Cdc42u were present in the proliferation zone while RhoB and Cdc42b were expressed only in the cortical plate where neural cells settle and differentiate. After birth, this isoform specificity quickly disappeared so that already at postnatal day 8 the adult pattern of expression was present. Our findings of a differential expression of the small GTP-binding proteins RhoA, RhoB, Cdc42u and Cdc42b in developing brain neocortex suggest isoform specific functions during neurogenesis and differentiation.

Cdc42: An essential Rho-type GTPase controlling eukaryotic cell polarity

Cdc42p is an essential GTPase that belongs to the Rho/Rac subfamily of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. The 11 current members of the Cdc42p family display between 75 and 100% amino acid identity and are functional as well as structural homologs. Cdc42p transduces signals to the actin cytoskeleton to initiate and maintain polarized gorwth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42p plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42p regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42p mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addition, Cdc42p has been implicated in a number of human diseases through interactions with its regulators and downstream effectors. While much is known about Cdc42p structure and functional interactions, little is known about the mechanism(s) by which it transduces signals within the cell. Future research should focus on this question as well as on the detailed analysis of the interactions of Cdc42p with its regulators and downstream effectors.