Journal of Genetics and Genomics

Lipidomics as a Principal Tool for Advancing Biomedical Research

Sin Man Lam, Guanghou Shui

2013, 40(8): 375-390. doi: 10.1016/j.jgg.2013.06.007

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Abstract:
Lipidomics, which targets at the construction of a comprehensive map of lipidome comprising the entire lipid pool within a cell or tissue, is currently emerging as an independent discipline at the interface of lipid biology, technology and medicine. The diversity and complexity of the biological lipidomes call for technical innovation and improvement to meet the needs of various biomedical studies. The recent wave of expansion in the field of lipidomic research is mainly attributed to advances in analytical technologies, in particular, the development of new mass spectrometric and chromatographic tools for the characterization and quantification of the wide array of diverse lipid species in the cellular lipidome. Here, we review some of the key technical advances in lipidome analysis and put forth the applications of lipidomics in addressing the biological roles of lipids in numerous disease models including the metabolic syndrome, neurodegenerative diseases and infectious diseases, as well as the increasing urgency to construct the lipidome inventory for various mammalian/organism models useful for biomedical research.

Rb Protein is Essential to the Senescence-Associated Heterochromatic Foci Formation Induced by HMGA2 in Primary WI38 Cells

Xi Shi, Baoqing Tian, Lingxia Liu, Yanyan Gao, Chi Ma, Namusamba Mwichie, Wenlong Ma, Liping Han, Baiqu Huang, Jun Lu, Yu Zhang

2013, 40(8): 391-398. doi: 10.1016/j.jgg.2013.05.007

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Abstract:
Cellular senescence is an irreversible form of cell cycle arrest that provides a barrier to neoplastic transformation. The integrity of the Rb (Retinoblastoma) pathway is necessary for the formation of the senescence-associated heterochromatin foci (SAHF) that offers a molecular basis for the stability of the senescent state. Surprisingly, although high mobility group A2 protein (HMGA2) can promote tumorigenesis and inhibit Rb function in tumor cells, high-level expression of HMGA2 is sufficient to induce SAHF formation in primary cells. It therefore becomes significant to determine whether Rb protein is necessary in HMGA2-induced SAHF formation. In this study, we established the cellular senescence and SAHF assembly WI38 cell model by ectopic expression of HMGA2, in which typical senescent markers were seen, including notable upregulation of p53, p21 and p16, and elevated SA-β-galactosidase staining together with downregulation of E2F target genes. We then showed that the Rb pathway inhibitor E7 protein was able to partly abolish the ability of SAHF formation after HMGA2 expression in WI38 cells, indicating that Rb is a crucial factor for HMGA2-induced SAHF formation. However, Rb depletion did not completely rescue the cell growth arrest induced by HMGA2, suggesting that Rb is not an exclusive pathway for HMGA2-induced senescence in WI38 cells.

Evolutionary and Functional Analysis of the Key Pluripotency Factor Oct4 and Its Family Proteins

Xinmin Zhang, Yuzhen Ma, Xiuying Liu, Qi Zhou, Xiu-Jie Wang

2013, 40(8): 399-412. doi: 10.1016/j.jgg.2013.04.011

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Abstract:
Oct4 is one of the key pluripotent factors essential for embryonic stem cells and induced pluripotent stem (iPS) cells. Oct4 belongs to the POU domain family, which contains multiples genes with various important functions. Although the function of Oct4 has been extensively studied, detailed comparison of Oct4 with other POU family genes and their evolutionary analysis are still lacking. Here, we systematically identified POU family genes from lower to higher animal species. We observed an expansion of POU family genes in vertebrates, with an additional increment in mammalian genomes. We analyzed the phylogenetic relationship, tissue specific expression profiles and regulatory networks of POU family genes of the human genome, and predicted the putative binding microRNAs of human POU family genes. These results provide the first comprehensive evolutionary and comparative analysis of POU family genes, which will help to better understand the relationships among POU family genes and shed light on their future functional studies.

Alteration of Terminal Heterochromatin and Chromosome Rearrangements in Derivatives of Wheat-Rye Hybrids

Shulan Fu, Zhenling Lv, Xiang Guo, Xiangqi Zhang, Fangpu Han

2013, 40(8): 413-420. doi: 10.1016/j.jgg.2013.05.005

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Abstract:
Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres. Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-Imperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat-rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny of a monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA (TTTAGGG)_n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives.

Functional Analysis of Autophagy Genes via Agrobacterium-Mediated Transformation in the Vascular Wilt Fungus Verticillium dahliae

Lei Zhou, Jun Zhao, Wangzhen Guo, Tianzhen Zhang

2013, 40(8): 421-431. doi: 10.1016/j.jgg.2013.04.006

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Abstract:
Autophagy is a widely conserved intracellular process for degradation and recycling of proteins, organelles and cytoplasm in eukaryotic organisms and is now emerging as an important process in foliar infection by many plant pathogenic fungi. However, the role of autophagy in soil-borne fungal physiology and infection biology is poorly understood. Here, we report the establishment of an Agrobacterium tumefaciens-mediated transformation (ATMT) system and its application to investigate two autophagy genes, VdATG8 and VdATG12, by means of targeted gene replacement and complementation. Transformation of a cotton-infecting Verticillium dahliae strain Vd8 with a novel binary vector pCOM led to the production of 384 geneticin-resistant transformants per 1 × 10⁶ conidia. V. dahliae mutants lacking either VdATG8 or VdATG12 exhibited reduced conidiation and impaired aerial hyphae production. Disease development on Arabidopsis plants was slightly delayed when inoculated with VdATG8 or VdATG12 gene deletion mutants, compared with the wild-type and gene complemented strains. Surprisingly, in vitro inoculation with unimpaired roots revealed that the abilities of root invasion were not affected in gene deletion mutants. These results indicate that autophagy is necessary for aerial hyphae development and plant colonization but not for root infection inV. dahliae.

Association of Renin Binding Protein (RnBP) Gene Polymorphisms with Essential Hypertension in the Hani Minority of Southwestern China

Yilong Dong, Yun Ding, Yina Cun, Chunjie Xiao

2013, 40(8): 433-436. doi: 10.1016/j.jgg.2013.06.002

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Abstract:

Structural and Expressional Variation Analyses of Mitochondrial Genomes Reveal Candidate Transcripts for the SV Cytoplasmic Male Sterility in Wheat (Triticum aestivum L.)

Junwei Wang, Xiaoli Wang, Hong Xu, Huiwu Tang, Gaisheng Zhang, Yao-Guang Liu

2013, 40(8): 437-439. doi: 10.1016/j.jgg.2013.03.004

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Abstract:

Genome-Wide Analysis of Gene Expression in Stationary Phase and Genetic Characterization of Stationary-Phase-Dependent Halocin Gene Expression in the Haloarchaeon Haloferax mediterranei

Xiaoqing Liu, Lei Wang, Jingfang Liu, Lei Cai, Hua Xiang

2013, 40(8): 441-444. doi: 10.1016/j.jgg.2013.04.009

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Abstract:

2013 Vol. 40, No. 8