Journal of Genetics and Genomics

Effects of SHIP-1 on MMP2 Secretion and Invasion of SR3Y1 Cells

Wanjin Xing, Michinari Hamaguchi

2007, 34(4): 285-293. doi: 10.1016/S1673-8527(07)60030-7

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Abstract:
SHIP-1 is an SH2 domain containing inositol-5-phosphatase that appears to be a negative regulator of hematopoiesis. To the potential effects of SHIP-1 on MMP2 secretion and migration of cancer cells, three murine SHIP-1 mutants were made: ΔSH2-SHIP-1, ΔPtase-SHIP-1, ΔCter-SHIP-1. These mutant forms were subcloned as well as the wild type (WT) of murine SHIP-1 cDNA were subcloned into pcDNA3 expression vector, then transfected into and overexpressed SHIP-1 and its mutants in a Src-transformed 3Y1 cell line (SR3Y1). The results showed that overexpression of wild type of SHIP-1 does not affect the MMP2 secretion in both SR3Y1 and 3Y1 cells, but can induce MMP9 secretion, while either WT SHIP-1, the SH2 domain, phosphatase domain, or C terminus deletion mutants could significantly block the MMP2 and MMP9 secretion in SR3Y1 cells and suppress cell invasion ability. The results confirmed SHIP-1 as a negative regulator for cell migration and invasion in transformed cells, and implied that it may function through each of its three domains.

Phylogenetic Reconstruction of the Family Acrypteridae (Orthoptera: Acridoidea) Based on Mitochondrial Cytochrome b Gene

Guangming Huo, Guofang Jiang, Zhengli Sun, Dianfeng Liu, Yalin Zhang, Lin Lu

2007, 34(4): 294-306. doi: 10.1016/S1673-8527(07)60031-9

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Abstract:
Sequences from the mitochondrial cytochrome b gene (Cyt b) were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony (MP) and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A + T and G + C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.

Detection of Quantitative Trait Loci Associated with Several Internal Organ Traits and Teat Number Trait in a Pig Population

Jinghu Zhang, Yuanzhu Xiong, Bo Zuo, Minggang Lei, Siwen Jiang, Feng'e Li, Rong Zheng, Jialian Li, Dequan Xu

2007, 34(4): 307-314. doi: 10.1016/S1673-8527(07)60032-0

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Abstract:
Quantitative trait loci (QTL) were detected for 8 internal organ traits, 3 carcass length traits, and teat number trait in 214 pigs in a resource population that included 180 F₂ individuals. A total of 39 microsatellite markers were examined on SSC4, SSC6, SSC7, SSC8, and SSC13. The genetic traits included heart weight (HW), lung weight (LW), liver and gallbladder weight (LGW), spleen weight (SPW), stomach weight (STW), small intestine weight (SIW), large intestine weight (LIW), kidney weight (KW), carcass length to the first cervical vertebra (CL1), carcass length to the first thoracic vertebra (CL2), rib numbers (RNS), and teat numbers (TNS). Results indicated that, 3 highly significant QTL (P ≤ 0.01 at chromosome-wise level) for HW (at 30 cM on SSC6), RNS (at 115 cM on SSC7), TNS (at 110 cM on SSC7), and 6 significant QTL (P ≤ 0.05 at chromosome-wise level) for LW (at 119 cM on SSC13), LGW (at 94 cM on SSC6), SPW (at 106 cM on SSC8), SIW (0 cM on SSC4), LIW (170 cM on SSC 4), and TNS (at 95 cM on SSC6) were detected. The phenotypic variances for which these QTL were accounted ranged from 0.04 % to 14.06 %. Most of these QTL had not been previously reported.

Structure of the Bovine ACAD8 Gene and the Association of Its Polymorphism with the Production Traits

Hengde Li, Shangzhong Xu, Xue Gao, Hongyan Ren

2007, 34(4): 315-320. doi: 10.1016/S1673-8527(07)60033-2

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Abstract:
Acyl-coenzyme A dehydrogenases (ACAD) are a family of nuclear-coded, mitochondrial flavoenzymes that catalyze the alpha, and beta-dehydrogenation of fatty acids. The eighth member of this family, ACAD8 catalyzes the valine catabolism. In this study, the bovine ACAD8 full-length mRNA and genomic DNA sequence were obtained and its gene structure was determined through alignment of the genomic DNA sequence to the mRNA sequence. The mRNA sequence consisted of a 1,251 bp open reading frame (ORF) flanked by a 37 bp 5′-untranslated region (UTR) and a 444 bp 3′-UTR; and its full-length genomic DNA sequence was 13,814 bp in length and included 11 exons and 10 introns. One A-G single nucleotide polymorphism (SNP) was revealed at nucleotide 13,408 (GenBank accession No. DQ435445) in the bovine ACAD8 gene by sequencing the polymerase chain reaction (PCR) products of 6 randomly selected individuals from the sample population. Different genotypes were determined by restriction fragment length polymorphism (RFLP). The association analysis of this SNP in bovine ACAD8 with production traits in 178 unrelated steers from 5 breeds showed that it had a significant effect on the daily gain and the beef tenderness (P < 0.05). Cattle with the G allele grew more rapidly and the beef they produced was more tender than those with the A allele. Thus, this SNP of the bovine ACAD8 gene can be used as an indicator to improve the growth rate and the beef tenderness.

Comparative Microsatellite Analysis of Grass Carp Genomes of Two Gynogenetic Groups and the Xiangjiang River Group

Kang Zheng, Kaidong Lin, Zhenghua Liu, Chen Luo

2007, 34(4): 321-330. doi: 10.1016/S1673-8527(07)60034-4

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Abstract:
The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group (Xiangjiang group), a one-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-1 group), and a two-generation artificially induced meio-gynogenetic grass carp group (meio-gynogenetic-2 group), were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.

Physiological Character and Gene Mapping in a New Green- revertible Albino Mutant in Rice

Tao Chen, Yadong Zhang, Ling Zhao, Zhen Zhu, Jing Lin, Suobing Zhang, Cailin Wang

2007, 34(4): 331-338. doi: 10.1016/S1673-8527(07)60035-6

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Abstract:
A green-revertible albino mutant-Qiufeng M was found from the japonica rice (Oryza sativa L. ssp. japonica) Qiufeng in the field. The first three leaves of the mutant were albino with some green. The leaf color became pale green since the fourth leaf and the glume had the same phenomenon as the first three leaves. The measuring data of the pigment content confirmed the visually observed results. It truly had a remarkable changing process in the leaf color in Qiufeng M. Comparison of the main agronomic characters between Qiufeng and Qiufeng M indicated that the neck length and grain weight showed significant difference at the 1% level, and other characters were not different. Genetic analysis showed that the green-revertible albino trait was controlled by a single recessive nucleic gene. Using 209 recessive mutant individuals in the F₂ population derived from the cross Pei'ai 64S × Qiufeng M, a gene, tentatively named gra, was located between the SSR markers of RM475 and RM2-22 on the long arm of chromosome 2. The genetic distance were 17.3 cM and 2.9 cM respectively.

Increased Endogenous Methyl Jasmonate Altered Leaf and Root Development in Transgenic Soybean Plants

Rengao Xue, Biao Zhang

2007, 34(4): 339-346. doi: 10.1016/S1673-8527(07)60036-8

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Abstract:
Methyl jasmonate (MeJA) is a plant-signaling molecule that regulates plant morphogenesis and expression of plant defense genes. To determine the role of the endogenous MeJA levels in the development of plants, transgenic soybean [Glycine max (L.) Merrill] plants harboringNTR1 gene encoding for jasmonic acid carboxyl methyltransferase (JMT) were produced. The activation of NTR1 gene expression resulted in the production of MeJA. Overexpression of the NTR1 cDNA under the regulation of cauliflower mosaic virus (CaMV) 35S promoter in the transgenic soybean plants was confirmed using Northern blot analysis. The significant differences in leaf and root growth patterns were observed between the transgenic plants and the wild-type plants. The leaves of the transgenic plants were slightly elongated in length but dramatically narrowed in width compared with the nontransformed wild-type plants. In addition, elongation of primary root was inhibited in the overexpressed transgenic soybean plantlets, whereas the development of lateral root was stimulated relative to the nontransformed plants. The leaves of the transgenic plants showed 2–2.5-fold higher levels of MeJA than the control plants. These results indicated that the increased endogenous levels of MeJA is involved in regulation of morphogenesis in soybean plants.

Molecular Characterization of Four ADF Genes Differentially Expressed in Cotton

Chengwei Zhang, Linlin Guo, Xiulan Wang, Hui Zhang, Haiyan Shi, Wenliang Xu, Xuebao Li

2007, 34(4): 347-354. doi: 10.1016/S1673-8527(07)60037-X

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Abstract:
Actin depolymerizing factor (ADF), highly conserved in all eukaryotic cells, is a low molecular mass of actin-binding protein, which plays a key role in modulating the polymerizing and depolymerizing of the actin filaments. Four cDNAs (designated GhADF2, GhADF3, GhADF4, and GhADF5, respectively) encoding ADF proteins were isolated from cotton (Gossypium hirsutum) fiber cDNA library. GhADF2 cDNA is 705 bp in length and deduces a protein with 139 amino acids. GhADF3 cDNA is 819 bp in length and encodes a protein of 139 amino acids. GhADF4 cDNA is 804 bp in length and deduces a protein with 143 amino acids. GhADF5 cDNA is 644 bp in length and encodes a protein of 141 amino acids. The molecular evolutionary relationship of these genes was analyzed by means of bioinformatics. GhADF2 is closely related to GhADF3 (99% identity) and PetADF2 (89% identity). GhADF4 is closely related to AtADF6 (78% identity), and GhADF5 is closely related to AtADF5 (83% identity). These results demonstrated that the plant ADF genes are highly conserved in structure. RT-PCR analysis showed that GhADF2 is predominantly expressed in fiber, whereas, GhADF5 is mainly expressed in cotyledons. On the other hand, it seems that GhADF3 and GhADF4 have no tissue specificity. Expression levels of different ADF genes may vary considerably in the same cell type, suggesting that they might be involved in regulating tissue development of cotton and the each ADF isoform may diverge to form the functional difference from the other ADFs during evolution.

Isolation and Characterization of CMO Gene Promoter from Halophyte Suaeda liaotungensis K.

Qiuli Li, Hui Yin, Dan Li, Hongfei Zhu, Yi Zhang, Weiwei Zhu

2007, 34(4): 355-361. doi: 10.1016/S1673-8527(07)60038-1

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Abstract:
The 5′-flanking proximal region of stress-induced gene encoding choline monooxygenase (CMO) was isolated by Adaptor-PCR and TAIL-PCR from halophyte Suaeda liaotungensis K. A total of 2,204 bp DNA sequence was obtained. The transcription start site, which is located at 128 bp upstream to the start ATG, was predicted by the TSSP-TCM program. The functional elements were analysed by PLACE program. The obtained SlCMO gene promoter contains the basic elements: TATA-box, CAAT-box, and stress-induced elements, for example, salt responsive element (GAAAAA), cold responsive elements (CANNTG), ABA (Abscisic Acid) responsive elements (NAACAA), water stress element (CGGTTG), and WUN responsive elements (GTTAGGTTC). Isolation and analysis of the promoter of the CMO gene from S. liaotungensis lays a foundation for characterising the stress-induced promoter elements, studying the relationship between the structure and function of the promoter, and investigating the molecular mechanism of CMO gene regulation.

An Entropy-based Index for Fine-scale Mapping of QTL

Yang Xiang, Yumei Li, Zaiming Liu, Zhenqiu Sun

2007, 34(4): 373-380. doi: 10.1016/S1673-8527(07)60040-X

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Abstract:
By comparing the entropy and conditional entropy in a marker, an entropy-based index for fine-scale linkage-disequilibrium gene mapping is presented using high-density marker maps in extreme samples for quantitative trait. The entropy-based index is the function of LD between the marker and the trait locus and does not depend on marker allele frequencies across the loci. It is parallel to Hardy-Weinberg disequilibrium (HWD) measure for QTL fine mapping, but its power of fine mapping QTL is higher than that of HWD measure. Through simulations, the fine mapping performance of this entropy-based index is investigated extensively under various genetic parameters. The results show that the indices presented here are both robust and powerful.

The Factors Shaping Synonymous Codon Usage in the Genome of Burkholderia mallei

Sheng Zhao, Qin Zhang, Zhihua Chen, Yixin Zhao, Jincheng Zhong

2007, 34(4): 362-372. doi: 10.1016/S1673-8527(07)60039-3

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Abstract:
Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ‘optimal codons’ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.

2007 Vol. 34, No. 4