Journal of Genetics and Genomics

Djrho2 is involved in regeneration of visual nerves in Dugesia japonica

Changxin Ma, Yang Gao, Guoliang Chai, Hanxia Su, Niejun Wang, Yigang Yang, Chunbo Li, Di Miao, Wei Wu

2010, 37(11): 713-723. doi: 10.1016/S1673-8527(09)60089-8

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Abstract:
The freshwater planarian is a powerful animal model for studying regeneration and stem cell activity in vivo. During regeneration, stem cells (neoblasts in planarian) migrated to the wounding edge to re-build missing parts of the body. However, proteins involved in regulating cell migration during planarian regeneration have not been studied extensively. Here we report two small GTPase genes (Djrho2 and Djrho3) of Dugesia japonica (strain Pek-1). In situ hybridization results indicated that Djrho2 was expressed throughout the body with the exception of the pharynx region while Djrho3 was specifically expressed along the gastro-vascular system. Djrho2 was largely expressed in neoblasts since its expression was sensitive to X-ray irradiation. In Djrho2-RNAi planarians, smaller anterior blastemas were observed in tail fragments during regeneration. Consistently, defective regeneration of visual nerve was detected by immunostainning with VC-1 antibody. These results suggested that Djrho2 is required for proper anterior regeneration in planairan. In contrast, no abnormality was observed after RNAi ofDjrho3. We compared protein compositions of control and Djrho2-RNAi planarians using an optimized proteomic approach. Twenty-two up-regulated and 26 de-regulated protein spots were observed in the two-dimensional electrophoresis gels, and 17 proteins were successfully identified by Mass Spectrometry (MS) analysis. Among them, 6 actin-binding or cytoskeleton-related proteins were found de-expressed in Djrho2-RNAi animals, suggesting that abnormal cytoskeleton assembling and cell migration were likely reasons of defected regeneration.

Gene expression changes in spleens of the wildlife reservoir species, Eurasian wild boar (Sus scrofa), naturally infected with Brucella suis biovar 2

Ruth C. Galindo, Pilar M. Muñoz, María J. de Miguel, Clara M. Marin, Javier Labairu, Miguel Revilla, José M. Blasco, Christian Gortazar, José de la Fuente

2010, 37(11): 725-736. doi: 10.1016/S1673-8527(09)60090-4

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Abstract:
Brucella suis is responsible for swine brucellosis worldwide. Of the five different B. suis biovars (bv.), bv. 2 appears restricted to Europe where it is frequently isolated from wild boar and hares, can infect pigs and can cause human brucellosis. In this study, the differential gene expression profile was characterized in spleens of Eurasian wild boar naturally infected with B. suis bv. 2. Of the 20,201 genes analyzed in the microarray, 633 and 1,373 were significantly (fold change > 1.8; P < 0.01) upregulated and downregulated, respectively, in infected wild boar. The analysis was focused on genes that were over represented after conditional test for biological process gene ontology. Upregulated genes suggested that B. suis bv. 2 infection induced cell maturation, migration and/or proliferation in infected animals. The genes downregulated in infected wild boar impaired the activity of several important cellular metabolic pathways such as metabolism, cytoskeleton organization and biogenesis, immune response and lysosomal function and vesicle-mediated transport. In addition, the response to stress, sperm fertility, muscle development and apoptosis seemed to be also impaired in infected animals. These results suggested thatB. suis bv. 2 may use strategies similar to other smooth brucellae to facilitate intracellular multiplication and the development of chronic infections. To our knowledge, this is the first report of the analysis of gene expression profile in hosts infected with B. suis bv. 2, which is important to understand the molecular mechanisms at the host-pathogen interface in the main reservoir species with possible implications in the zoonotic cycle of the pathogen.

Generality and characteristics of genetic and epigenetic changes in newly synthesized allotetraploid wheat lines

Bao Qi, Xiaofang Zhong, Bo Zhu, Na Zhao, Liying Xu, Huakun Zhang, Xiaoming Yu, Bao Liu

2010, 37(11): 737-748. doi: 10.1016/S1673-8527(09)60091-6

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Abstract:
Previous studies have shown rapid and extensive genomic instability associated with early stages of allopolyploidization in wheat. However, these studies are based on either a few pre-selected genomic loci or genome-wide analysis of a single plant individual for a given cross combination, thus making the extent and generality of the changes uncertain. To further study the generality and characteristics of allopolyploidization-induced genomic instability in wheat, we investigated genetic and epigenetic changes from a genome-wide perspective (by using the AFLP and MSAP markers) in four sets of newly synthesized allotetraploid wheat lines with various genome constitutions, each containing three randomly chosen individual plants at the same generation. We document that although general chromosomal stability was characteristic of all four sets of allotetraploid wheat lines, genetic and epigenetic changes at the molecular level occurred in all these plants, with both kinds of changes classifiable into two distinct categories, i.e., stochastic and directed. The abundant type of genetic change is loss of parental bands while the prevalent cytosine methylation pattern alteration is hypermethylation at the CHG sites. Our results have extended previous studies regarding allopolyploidization-induced genomic dynamics in wheat by demonstrating the generality of both genetic and epigenetic changes associated with multiple nascent allotetraploid wheat lines, and providing novel insights into the characteristics of the two kinds of induced genomic instabilities.

Genome-wide transcriptional analysis of maize endosperm in response to ae wx double mutations

Xiang Li, Guang Hui Chen, Wei Yang Zhang, Xiansheng Zhang

2010, 37(11): 749-762. doi: 10.1016/S1673-8527(09)60092-8

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Abstract:
Starch biosynthesis is important during endosperm development. Much has been known for the regulation of gene expression involved in starch synthesis, less information is available on the genome-wide expression profiles as a consequence of impaired starch synthesis. In this study, we examined the transcriptional responses through microarray analysis in an ae wx double-mutant with loss-of-function starch branching enzyme IIb (SBEIIb) and granule-bound starch synthase I (GBSSI). Through Gene Ontology enrichment analysis, we identified differentially expressed genes (DEGs) involved in chromatin organization and lipid transport. The DEGs also include alcohol dehydrogenase genes and pyruvate decarboxylase genes involved in sugar metabolism. In summary, the ae wx double mutations caused pleiotropic effects and transcriptional changes for a number of genes involved in metabolism, cellular response and organization. Therefore, a block in starch synthesis triggers transcriptional responses to favour the flux of excess carbohydrates into glycolysis, pentose phosphate pathway, and cell wall biosynthesis, but not toward the synthesis of alternative storage compounds.

Species authentication of commercial beef jerky based on PCR-RFLP analysis of the mitochondrial 12S rRNA gene

Shi-Yi Chen, Yi-Ping Liu, Yong-Gang Yao

2010, 37(11): 763-769. doi: 10.1016/S1673-8527(09)60093-X

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Abstract:
In this study, we determined species-specific variations by analyzing the mitochondrial 12S rRNA gene sequence variation (∼440 bp) in 17 newly obtained sequences and 90 published cattle, yak, buffalo, goat, and pig sequences, which represent 62 breeds and 17 geographic regions. Based on the defined species-specific variations, two endonucleases, Alu I and Bfa I, were selected for species authentication using raw meat/tissue samples and the PCR-RFLP method. Goat and pig were identified using the Alu I enzyme, while cattle, yak, and buffalo were identified by digestion with Bfa I. Our approach had relatively high detection sensitivity of cattle DNA in mixed cattle and yak products, with the lowest detectable threshold equaling 20% of cattle DNA in a mixed cattle/yak sample. This method was successfully used to type commercial beef jerky products, which were produced by different companies utilizing various processing technologies. Our results show that several yak jerky products might be implicated in commercial fraud by using cattle meat instead of yak meat.

2010 Vol. 37, No. 11