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Biochemical Genetics (v.44, #3-4)

Genetic Variations of 13 Indigenous Chinese Goat Breeds Based on Cytochrome b Gene Sequences by Shilin Chen; Bin Fan; Bang Liu; Mei Yu; Shuhong Zhao; Mengjin Zhu; Tongan Xiong; Kui Li (pp. 87-97).

Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F _st=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.

Keywords: phylogeny relationship; genetic variability; Cyt b gene; Chinese goat.

Isolation and Sequence Analysis of the Sox-1, -2, -3 Homologs in Trionyx sinensis and Alligator sinensis Having Temperature-Dependent Sex Determination by Jifang Zheng; Muyuan Zhu (pp. 98-109).

Members of the Sox gene family are characterized by an HMG-box that shows sequence similarity with that of the mouse testis-determining gene Sry. Using degenerate primers PCR, seven and eight HMG-box motifs of Sry-related genes were cloned and sequenced from genomic DNA of Trionyx sinensis (termed TS41-47) and Alligator sinensis (AS41-48) with TSD (temperature-dependent sex determination). Among 15 Sry-related genes, TS41, TS42, AS41, and AS42 shared 80, 72, 81, and 79% amino acid identity, respectively, with each HMG-box domain of the mouse Sox-1, -2, and -3 genes by Blast analysis. Molecular phylogenetic analysis showed that the clustering of TS41-42 and AS41-42 was distant to the clustering of the nonreptilian vertebrate Sox-1, -2, -3 homologs, including fish, amphibian, bird, and mammals. The amino acid identity among TS41-42, AS41-42, and the nonreptilian vertebrate Sox-1, -2, -3 homologs is lower than identities among the Sox-1, -2, -3 homologs, suggesting that the sequence changes in TS41-42 of Trionyx sinensis and AS41-42 of Alligator sinensis might have occurred after the diversification of amniotes.

Keywords: Sox gene; Sry ; evolution; cloning; reptile

Major Histocompatibility Complex Variation in the Endangered Crested Ibis Nipponia nippon and Implications for Reintroduction by Bei Zhang; Sheng-Guo Fang; Yong-Mei Xi (pp. 110-120).

The major histocompatibility complex (MHC), with its extraordinary levels of genetic variation, is thought to be an essential aspect of the ability of an organism to recognize different parasites and pathogens. It has also been proposed to regulate reproductive processes in many aspects. Here we examine the genetic variation of the second exon of the MHC class II B genes of the crested ibis, an endangered species known to descend from just two breeding pairs rediscovered in 1981. Only five alleles are identified by single-strand conformation polymorphism (SSCP) analysis of 36 samples taken from both wild and captive populations, and a comparatively low level of divergence between MHC alleles is observed. We suggest that representative sampling of individuals with most of the different MHC allele genotypes to constitute a founder population, together with the monitoring of the pathogen status of candidate sites before release, is of great importance for raising the success rate of reintroduction for the crested ibis.

Keywords: Genetic diversity; population bottleneck; conservation; SSCP

Identification and Characterization of LIW, a Novel Domain Involved in Animal NCKIPSDs and Some Uncharacterized Fungal Proteins by Wei Huang; Xuhui Lai; Honghai Wang; Shouyuan Zhao; Jinhu Guo; Chaoqun Wu (pp. 121-128).

Optimized RT-PCR Method for Assaying Expression of Monocyte Chemotactic Protein Type 1 (MCP-1) in Rabbit Aorta by B. Sękalska; A. Ciechanowicz; B. Dołęgowska; M. Naruszewicz (pp. 129-139).

The reverse transcription polymerase chain reaction (RT-PCR) is one of the most useful molecular biology methods in opening the way to understanding of the mechanisms of atherosclerosis on the gene structure and/or expression level. We optimized this technique for assaying expression of the monocyte chemotactic protein type 1 (MCP-1) gene in rabbit aorta with respect to the temperature profile, yield to cycle number, interference of genomic DNA with the RNA matrix, and repeatability. Variability of expression of the constitutive GAPDH gene was also examined. The study was done in 18 New Zealand rabbits allocated to two groups and fed a standard chow for 2 (S1) or 3 (S2) months. The experiment ended with removal of part of the ascending rabbit aorta, from which RNA was isolated. The optimal temperature for binding of specific primers to the MCP-1 and GAPDH genes was 63°C, and the optimal number of cycles for PCR amplification was 22 for MCP-1 and 26 for GAPDH. The GAPDH amplicon size was 465 base pairs in the presence or absence of reverse transcriptase showing contamination of the RNA matrix with genomic DNA. Repeatability of the RT-PCR method was 8.7%, and variability of expression of the GAPDH gene was 7.7%. Thus, RT-PCR adjusted for contaminating genomic DNA provides a reliable way of assaying expression of the MCP-1 gene in rabbit aorta.

Keywords: polymerase chain reaction; reverse transcription; monocyte chemotactic protein type 1; atherosclerosis

The Structure and Diversity of α₁-Acid Glycoprotein/Orosomucoid Gene in Africans by Isao Yuasa; Hiroaki Nakamura; Kazuo Umetsu; Yoshito Irizawa; Lotte Henke; Jürgen Henke (pp. 140-155).

Human orosomucoid (ORM), or α₁-acid glycoprotein, is known to be controlled by duplicated and triplicated genes on chromosome 9, encoding ORM1 and ORM2 proteins. In this study, the structure and diversity of the ORM gene were investigated in 16 Sub-Saharan Africans, who originated from widely dispersed locations in Africa. The duplicated ORM1-ORM2 gene was observed in all 16 samples. ORM1*S1(2), characterized by an ORM2 gene-specific sequence in intron 5, was common in Africans. Three Africans showed the duplication of the ORM1 gene. The organization of the triplicated ORM1A-ORM1B-ORM2 gene was established in two Africans. The recombination breakpoints resulting in the ORM1 duplication lay within a small genomic interval around exon 1 of the ORM1B gene. The duplication of the ORM2 gene reported previously was not detected in this population sample. Several single-nucleotide polymorphisms were observed in the ORM2 gene. The rearrangement of the ORM gene is likely to occur often in Africans.

Keywords: α₁-acid glycoprotein; African; gene rearrangement; genomic structure; orosomucoid

Genetic Diversity of Chinese Water Deer (Hydropotes inermis inermis): Implications for Conservation by Jie Hu; Sheng-Guo Fang; Qiu-Hong Wan (pp. 156-167).

The Chinese water deer (Hydropotes inermis inermis) is endemic to China. Historically, the species was widely distributed, but now, habitat loss and poaching have reduced its range and number drastically. In order to provide useful information for its conservation, we have investigated the genetic diversity and population structure of the Chinese water deer by analyzing the 403 bp fragment of the mitochondrial DNA (mtDNA) control region (D-loop). Eighteen different haplotypes were detected in 40 samples. Overall, Chinese water deer have a relatively high-genetic diversity compared to other rare cervid species, with a haplotype diversity of 0.923±0.025 and nucleotide diversity of 1.318 ± 0.146%. No obvious phylogenetic structure among haplotypes was found for samples of different origin. An analysis of molecular variance (AMOVA) showed significant differentiation between the Zhoushan and the mainland population (F_ST= 0.088, P < 0.001; Φ ST = 0.075, P = 0.043), which suggests that exchanges of individuals between Zhoushan and the mainland should be avoided. We also recommend that a breeding center be set up for the mainland population.

Keywords: Hydropotes inermis inermis ; diversity; mitochondrial DNA; D-loop; conservation strategies

Comparison of HCMV IE and EF-1 Promoters for the Stable Expression of β-Subunit of Hexosaminidase in CHO Cell Lines by Incilay Sinici; Maryam Zarghooni; Michael B. Tropak; Don J. Mahuran; H. Asuman Özkara (pp. 168-175).

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Biochemical Genetics (v.44, #3-4)

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Biochemical Genetics (v.44, #3-4)