5.9
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5.9
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2009 Vol. 36, No. 10

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Research article
A zebrafish gene trap line expresses GFP recapturing expression pattern of foxj1b
Tian Tian, Long Zhao, Xinyi Zhao, Min Zhang, Anming Meng
2009, 36(10): 581-589. doi: 10.1016/S1673-8527(08)60150-2
Abstract (75) HTML PDF (0)
Abstract:
Foxj1 has been found to play an important role in cilia formation and function in vertebrates. The zebrafish or Xenopus genome expresses two Foxj1 genes, foxj1a/FoxJ1 and foxj1b/FoxJ1.2. In this study, we have generated a zebrafish transgenic line T2BGSZ10 by To l 2 transposon-based gene trapping approach. T2BGSZ10 transgenic fish carry an insertion of the transposon genome into the first intron of the foxj1b locus. This insertion results in GFP expression in the forebrain, otic vesicles, floorplate, pronephric ducts and other domains during embryogenesis, which recaptures the expression pattern of foxj1b. Although normal expression of foxj1b is dramatically reduced, T2BGSZ10 homozygous embryos develop normally and grow to adulthood without detectable defects, which may be due to the incomplete interruption of foxj1b expression. Nevertheless, this transgenic line may serve as a useful model for dynamic observation of GFP-labeled tissues and organs and for isolation of GFP-labeled cells.
Bioinformatic analysis of microRNA biogenesis and function related proteins in eleven animal genomes
Xiuying Liu, GuanZheng Luo, Xiujuan Bai, Xiu-Jie Wang
2009, 36(10): 591-601. doi: 10.1016/S1673-8527(08)60151-4
Abstract (68) HTML PDF (0)
Abstract:
MicroRNAs are ∼22 nt long small non-coding RNAs that play important regulatory roles in eukaryotes. The biogenesis and functional processes of microRNAs require the participation of many proteins, of which, the well studied ones are Dicer, Drosha, Argonaute and Exportin 5. To systematically study these four protein families, we screened 11 animal genomes to search for genes encoding above mentioned proteins, and identified some new members for each family. Domain analysis results revealed that most proteins within the same family share identical or similar domains. Alternative spliced transcript variants were found for some proteins. We also examined the expression patterns of these proteins in different human tissues and identified other proteins that could potentially interact with these proteins. These findings provided systematic information on the four key proteins involved in microRNA biogenesis and functional pathways in animals, and will shed light on further functional studies of these proteins.
Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events
Jun Lin, Yihuai Hu, Bing Tian, Yuejin Hua
2009, 36(10): 603-610. doi: 10.1016/S1673-8527(08)60152-6
Abstract (96) HTML PDF (0)
Abstract:
The MutT/Nudix superfamily proteins repair DNA damage and play a role in human health and disease. In this study, we examined two different cases of double MutT/Nudix domain-containing proteins from eukaryotes and prokaryotes. Firstly, these double domain proteins were discovered in Drosophila, but only single Nudix domain proteins were found in other animals. The phylogenetic tree was constructed based on the protein sequence of Nudix_N and Nudix_C fromDrosophila, and Nudix from other animals. The phylogenetic analysis suggested that the double Nudix domain proteins might have undergone a gene duplication-speciation-fusion process. Secondly, two genes of the MutT family, DR0004 and DR0329, were fused by two mutT gene segments and formed double MutT domain protein genes in Deinococcus radiodurans. The evolutionary tree of bacterial MutT proteins suggested that the double MutT domain proteins in D. radiodurans probably resulted from a gene duplication-fusion event after speciation. Gene duplication-fusion is a basic and important gene innovation mechanism for the evolution of double MutT/Nudix domain proteins. Independent gene duplication-fusion events resulted in similar domain architectures of different double MutT/Nudix domain proteins.
Analysis of expressed receptor-like kinases (RLKs) in soybean
Peng Liu, Wei Wei, Shouqiang Ouyang, Jin-Song Zhang, Shou-Yi Chen, Wan-Ke Zhang
2009, 36(10): 611-619. doi: 10.1016/S1673-8527(08)60153-8
Abstract (62) HTML PDF (2)
Abstract:
Receptor-like kinases (RLKs) play crucial roles in cellular signal perception and propagation. To study the evolutionary relationships among RLKs in soybean, a large-scale expressed sequence tags (ESTs) survey for RLKs-related sequences was conducted. By doing BLAST analysis using our database and The Gene Index Database, 605 putative RLK genes were identified. Based on the phylogeny of the kinase domain, these soybean RLKs were classified into 58 different small subfamilies. The phylogenetic analysis of RLKs in soybean, rice and Arabidopsis showed that different subfamilies of RLKs had different functions and could have experienced different selective pressures.
Distinguishing transgenic from non-transgenic Arabidopsis plants by 1H NMR-based metabolic fingerprinting
Yanfei Ren, Tao Wang, Yufa Peng, Bin Xia, Li-Jia Qu
2009, 36(10): 621-628. doi: 10.1016/S1673-8527(08)60154-X
Abstract (69) HTML PDF (2)
Abstract:
We have recently reported the construction of an nuclear magnetic resonance (NMR)-based metabonomics study platform, Automics. To examine the application of Automics in transgenic plants, we performed metabolic fingerprinting analysis, i.e., 1H NMR spectroscopy and multivariate analysis, on wild-type and transgenicArabidopsis. We found that it was possible to distinguish wild-type from four transgenic plants by PLS-DA following application of orthogonal signal correction (OSC). Scores plot following OSC clearly demonstrates significant variation between the transgenic and non-transgenic groups, suggesting that the metabolic changes among wild-type and transgenic lines are possibly associated with transgenic event. We also found that the major contributing metabolites were some specific amino acids (i.e., threonine and alanine), which could correspond to the insertion of the selective marker BAR gene in the transgenic plants. Our data suggests that NMR-based metabonomics is an efficient method to distinguish fingerprinting difference between wild-type and transgenic plants, and can potentially be applied in the bio-safety assessment of transgenic plants.
A comparative proteomics approach to detect unintended effects in transgenic Arabidopsis
Yanfei Ren, Jun Lv, Hua Wang, Linchuan Li, Yufa Peng, Li-Jia Qu
2009, 36(10): 629-639. doi: 10.1016/S1673-8527(08)60155-1
Abstract (58) HTML PDF (0)
Abstract:
Recently, as part of biosafety assessments, unintended effects have been given much attention. In this study, we applied a proteomics approach to elucidate the unintended effects of random T-DNA insertion in transgenic plants. Separated proteins extracted from 12 trans-genic Arabidopsis thaliana with different T-DNA insertion sites and from wild-type (ecotype Col-o) were analyzed. In the transgenic plants, 102 significantly altered protein spots were detected, in which 59 were up-regulated and 43 down-regulated. MALDI-TOF MS analysis showed that most of these expression level-altered proteins were involved in energy transfer, oxidative respiration and photosynthesis. However, none of these proteins was a toxic protein or allergen. Using plants with or without cold treatment, a natural environmental stress, as controls, we found that the number of the altered proteins was even less in those transgenic plants than those triggered by the cold treatment, suggesting that the transgenic events had a weaker impact on the plants than the environmental stresses. Interestingly, the phosphinothricin acetyl transferase (PAT), theBAR-encoded protein, was detected in nine out of twelve different T-DNA insertion lines at five different insertion sites. These data suggest that the most significant impact of transgenic events on the host plants is from the transgene itself, i.e., from the predictable intended effects, rather than unintended effects. This study also suggests that the proteomics approach has the potential to detect the unintended effects in transgenic plants.
Instructions for authors
2009, 36(10): 641-644. doi: 10.1016/S1673-8527(09)60019-9
Abstract (47) HTML PDF (0)
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