Journal of Genetics and Genomics

The 7th Editoral Board of Journal of Genetics and Genomics

2008, 35(1): i-iv. doi: 10.1016/S1673-8527(08)60009-0

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New players in the regulation of ecdysone biosynthesis

Xun Huang, James T. Warren, Lawrence I. Gilbert

2008, 35(1): 1-10. doi: 10.1016/S1673-8527(08)60001-6

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Insect ecdysone steroid hormone regulates major developmental transitions, such as molting and metamorphosis. The production of ecdysone correlates well with the timing of these transitions. Finding out how the ecdysone biosynthesis is regulated is crucial to fully understand these sophisticated developmental switches. Here we summarized recent findings in the regulation of ecdysone biosynthesis from the aspects of cell signaling, key biosynthetic enzymes and substrate cholesterol trafficking.

Chromosome analysis of esophageal squamous cell carcinoma cell line KYSE 410-4 by repetitive multicolor fluorescence in situ hybridization

Yiling Yang, Jiayou Chu, Yupeng Wu, Manli Luo, Xin Xu, Yaling Han, Yan Cai, Qimin Zhan, Mingrong Wang

2008, 35(1): 11-16. doi: 10.1016/S1673-8527(08)60002-8

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Chromosome aberrations are distinctive features of human malignant tumors. Analysis of chromosomal changes can illuminate the molecular mechanisms underlying the development and progression of cancer. To establish the technique of multicolor fluorescence in situ hybridization (M-FISH) for identifying chromosome aberrations in esophageal carcinoma cell line KYSE 410-4, four pools of 6-color whole-chromosome painting probes have been designed and hybridized on the same metaphase spread by four rounds of repetitive FISH. Repetitive 6-color M-FISH was successfully established and the cytogenetic abnormalities in KYSE 410-4 cells were characterized. Chromosome gains occurred at 2q, 3, 8, 17p, and X. An isochromosome 3q was visualized in the cell line, which might be one intermediate mechanism leading to 3p losses and/or 3q gains. Furthermore, 16 structural arrangements were detected, including four derivative chromosomes. The rearrangement of the centromeric regions accounted for approximately 44% of all rearrangements. The results added a more complete and accurate information of the genetic alterations to the classical cytogenetic description of KYSE 410-4 and provided a detailed cytogenetic background data for appropriate use of the cell line. The established 6-color M-FISH was useful for analyzing chromosomes in the whole genome of human tumors.

Bioinformatic identification of genes encoding C1q-domain-containing proteins in zebrafish

Jie Mei, Jianfang Gui

2008, 35(1): 17-24. doi: 10.1016/S1673-8527(08)60003-X

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C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immunities. The globular (gC1q) domain similar with C1q was also found in many non-complement C1q-domain-containing (C1qDC) proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor (TNF) ligand family, and also have diverse functions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through comprehensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-containing (C1qDC) proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q domain. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.

The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

Yongjiang Mao, Hong Chang, Zhangping Yang, Liu Zhang, Ming Xu, Guobin Chang, Wei Sun, Guangming Song, Dejun Ji

2008, 35(1): 25-32. doi: 10.1016/S1673-8527(08)60004-1

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A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by (δμ)² and DA distances, and the divergence times between populations were estimated by (δμ)². Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas, Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039–0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501–1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136–0.363, 0.273–0.729, and 0.326–0.600 MYA, respectively.

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

Li Zhang, Liuwang Nie, Chenghe Cao, Ying Zhan

2008, 35(1): 33-40. doi: 10.1016/S1673-8527(08)60005-3

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The complete mitochondrial genome (16,837 bp) from the Keeled box turtle (Pyxidea mouhotii) was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule: a large number of (ATTATATC) _n direct tandem repeats followed by (TA) _n microsatellite at the 3′ end of the control region (D-loop), which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood (ML) and Bayesian (BI) analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1) Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group (containing Pyxidea) may have originated from two ancestors; 2) the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.

Analysis of DNA methylation in different maize tissues

Yanli Lu, Tingzhao Rong, Moju Cao

2008, 35(1): 41-48. doi: 10.1016/S1673-8527(08)60006-5

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DNA methylation plays an important role in gene expression regulation during biological development and tissue differentiation in plants. This study adopted methylation-sensitive Amplified fragment length polymorphism (AFLP) to compare the levels of DNA cytosine methylation at CCGG sites in tassel, bracteal leaf, and ear leaf from maize inbred lines, 18 White and 18 Red, respectively, and also examined specific methylation patterns of the three tissues. Significant differences in cytosine methylation level among the three tissues and the same changing tendency in two inbred lines were detected. Both MSAP (methylation sensitive amplification polymorphism) ratio and full methylation level were the highest in bracteal leaf, and the lowest in tassel. Meanwhile, different methylation levels were observed in the same tissue from the inbred lines, 18 White and 18 Red. Full methylation of internal cytosine was the dominant type in the maize genome. The differential methylation patterns in the three tissues were observed. In addition, sequencing of nine differentially methylated fragments and the subsequent blast search revealed that the cytosine methylated 5′ -CCGG-3′ sequences were distributed in repeating sequences, in the coding and noncoding regions. Southern hybridization was used to verify the methylation polymorphism. These results clearly demonstrated the power of the MSAP technique for large-scale DNA methylation detection in the maize genome, and the complexity of DNA methylation change during plant growth and development. The different methylation levels may be related to specific gene expression in various tissues.

Identification of differentially expressed proteins in poplar leaves induced by Marssonina brunnea f. sp. Multigermtubi

Kun Yuan, Bo Zhang, Yanmei Zhang, Qiang Cheng, Mingxiu Wang, Minren Huang

2008, 35(1): 49-60. doi: 10.1016/S1673-8527(08)60007-7

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Black spot disease in poplar is a disease of the leaf caused by fungus. The major pathogen is Marssonina brunnea f. sp. multigermtubi. To date, little is known about the molecular mechanism of poplar (M. brunnea) interaction. In order to identify the proteins related to disease resistance and understand its molecular basis, the clone “NL895” (P. euramericana CL“NL895”), which is highly resistant to M. brunnea f. sp. multigermtubi, was used in this study. We used two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) to identify the proteins in poplar leaves that were differentially expressed in response to black spot disease pathogen, M. brunnea f. sp. multigermtubi. Proteins extracted from poplar leaves at 0, 12, 24, 48, and 72 h after pathogen-inoculation were separated by 2-DE. About 500 reproducible protein spots were detected, of which 40 protein spots displayed differential expression in levels and were subjected to Matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) followed by database searching. According to the function, the identified proteins were sorted into five categories, that is, protein synthesis, metabolism, defense response and unclassified proteins.

Instructions for authors

2008, 35(1): 61-64. doi: 10.1016/S1673-8527(08)60008-9

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2008 Vol. 35, No. 1