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Biochemical Genetics (v.49, #5-6)

Alternative Splicing of Human Height-Related Zinc Finger and BTB Domain-Containing 38 Gene Through Alu Exonization by Kyung-Won Hong; Young-Bin Shin; Hyun-Seok Jin; Ji-Eun Lim; Je-Yong Choi; Kyu-Tae Chang; Heui-Soo Kim; Bermseok Oh (pp. 283-291).

Recently, genome-wide association studies have identified a strong association between the ZBTB38 locus and human height. In a functional study, we detected two RT-PCR products of ZBTB38, amplified with primers in exons 7 and 8 from a chondrocyte cell line, C-28/I2. Sequencing revealed that the longer product contained an Alu segment in intron 7 of ZBTB38, which contained a potential splicing acceptor site that likely was used to generate the alternative transcript. Insertion of the Alu segment changed the consensus Kozak sequence of the ZBTB38 transcript, potentially altering translational efficiency. We performed RT-PCR using 16 tissue samples from humans and 8 tissue samples from primates to determine any tissue specificity or evolutionary conservation of the alternative splicing. Although we failed to identify any difference among the tissues, all primate samples expressed only the shorter Alu segment (lacking the transcript), suggesting that the alternative splicing event is hominid primate-specific.

Keywords: ZBTB38 ; Alternative splicing; Alu; Exonization; Height

Haplotypes in the Interleukin 8 Gene and Their Association with Chronic Periodontitis Susceptibility by Raquel M. Scarel-Caminaga; Yeon J. Kim; Aline C. Viana; Karen M. C. Curtis; Sâmia C. T. Corbi; Patrícia M. Sogumo; Silvana R. P. Orrico; Joni A. Cirelli (pp. 292-302).

Interleukin-8 (IL-8), which is responsible for the migration and activation of neutrophils, is an important inflammatory mediator involved in the initiation and amplification of acute inflammatory reactions and chronic inflammatory processes. IL-8 plays an important role in periodontitis, an inflammatory disease characterized by the loss of connective tissue and alveolar bone. The aim of this study was to investigate whether the SNPs rs2227307 (+396) and rs2227306 (+781), and the haplotypes they formed together with the previously investigated rs4073 (−251), were associated with chronic periodontitis susceptibility. Clinical periodontal exams were performed and DNA samples were collected from 493 individuals (223 with periodontitis and 270 controls). Associations between SNPs, haplotypes, and subject phenotypes were analyzed using the χ² test followed by multivariate logistic regression modeling. We conclude that the +396TT genotype and the haplotypes ATC/TTC and AGT/TGC were significantly associated with chronic periodontitis susceptibility in Brazilians.

Keywords: Interleukin 8; Periodontitis; Polymorphism; Disease susceptibility

Populationwide Investigation of Two Indel Polymorphisms at the Prion Protein Gene in Polish Holstein–Friesian Cattle by Urszula Czarnik; Janusz Strychalski; Tadeusz Zabolewicz; Chandra S. Pareek (pp. 303-312).

The allele, genotype, and haplotype frequencies among 837 Polish Holstein–Friesian cattle were determined at two regulatory indel polymorphisms of the PRNP gene. Allele frequencies at the 23 bp indel promoter polymorphism were 0.622 (del) and 0.378 (ins), with 0.613 and 0.387 in sires and 0.633 and 0.366 in dams. Allele frequencies at the 12 bp indel intron polymorphism were 0.527 (del) and 0.473 (ins), with 0.529 and 0.471 in sires and 0.543 and 0.456 in dams. Four haplotypes were identified in this population (23–12del, 23–12ins, 23del–12ins, and 23ins–12del). Haplotype 23–12del occurred most frequently in both sire and dam groups. Comparative analysis of Polish Holstein–Friesian and German Holstein populations revealed a similar genetic structure for the 23 bp indel polymorphism and a significantly different one for the 12 bp indel polymorphism. In allele and haplotype analysis, significant differences were observed between the Polish Holstein–Friesian population and a BSE-free German Holstein population.

Keywords: Holstein–Friesian cattle; PRNP gene; Indel polymorphisms

Evaluation of RPE65, CRALBP, VEGF, CD68, and Tyrosinase Gene Expression in Human Retinal Pigment Epithelial Cells Cultured on Amniotic Membrane by Hassan Akrami; Zahra-Soheila Soheili; Majid Sadeghizadeh; Keynoush Khalooghi; Hamid Ahmadieh; Mojgan Rezaie Kanavi; Shahram Samiei; Jalil Pakravesh (pp. 313-322).

The retinal pigment epithelium (RPE) plays a key role in the maintenance of the normal functions of the retina. Tissue engineering using amniotic membrane as a substrate to culture RPE cells may provide a promising new strategy to replace damaged RPE. We established a method of culturing RPE cells over the amniotic membrane as a support for their growth and transplantation. The transcription of specific genes involved in cellular function of native RPE, including RPE65, CRALBP, VEGF, CD68, and tyrosinase, were then measured using quantitative real-time PCR. Data showed a considerable increase in transcription of RPE65, CD68, and VEGF in RPE cells cultured on amniotic membrane. The amounts of CRALBP and tyrosinase transcripts were not affected. This may simply indicate that amniotic membrane restricted dedifferentiation of RPE cells in culture. The results suggest that amniotic membrane may be considered as an elective biological substrate for RPE cell culture.

Keywords: Retinal pigment epithelium; Amniotic membrane; Age-related macular degeneration; Cell culture; Gene expression

Kell Blood Group System Polymorphism in an Urban Tunisian Population by Meriem Bani; Houda Kaabi; Mohamed Hichem Sellami; Manel Chaabane; Ghaya Cherif; Hedi Bellali; Brahim Midouni; Nejia Chalfouh; Amel Dridi; Afef Jeridi; Slama Hmida (pp. 323-328).

Regulation of Hemocytes in Drosophila Requires dappled Cytochrome b5 by Kurt Kleinhesselink; Corinna Conway; David Sholer; Irvin Huang; Deborah A. Kimbrell (pp. 329-351).

A major category of mutant hematopoietic phenotypes in Drosophila is melanotic tumors or nodules, which consist of abnormal and overproliferated blood cells, similar to granulomas. Our analyses of the melanotic mutant dappled have revealed a novel type of gene involved in blood cell regulation. The dappled gene is an essential gene that encodes cytochrome b5, a conserved hemoprotein that participates in electron transfer in multiple biochemical reactions and pathways. Viable mutations of dappled cause melanotic nodules and hemocyte misregulation during both hematopoietic waves of development. The sexes are similarly affected, but hemocyte number is different in females and males of both mutants and wild type. Additionally, initial tests show that curcumin enhances the dappled melanotic phenotype and establish screening of endogenous and xenobiotic compounds as a route for analysis of cytochrome b5 function. Overall, dappled provides a tractable genetic model for cytochrome b5, which has been difficult to study in higher organisms.

Keywords: Hemocytes; dappled ; Cytochrome b5; Melanotic tumors; Granulomas

Molecular Characterization of High Plant Species Using PCR with Primers Designed from Consensus Branch Point Signal Sequences by Faqian Xiong; Jing Jiang; Zhuqiang Han; Ruichun Zhong; Liangqiong He; Weijian Zhuang; Ronghua Tang (pp. 352-363).

A novel method is introduced for producing molecular markers in plants using single 15- to 18-mer PCR primers designed from the short conserved consensus branch point signal sequences and standard agarose gel electrophoresis. This method was tested on cultivated peanut and verified to give good fingerprinting results in other plant species (mango, banana, and longan). These single primers, designed from relatively conserved branch point signal sequences within gene introns, should be universal across other plant species. The method is rapid, simple, and efficient, and it requires no sequence information of the plant genome of interest. It could be used in conjunction with, or as a substitute for, conventional RAPD or ISSR techniques for applications including genetic diversity analysis, phylogenetic tree construction, and quantitative trait locus mapping. This technique provides a new way to develop molecular markers for assessing genetic diversity of germplasm in diverse species based on conserved branch point signal sequences.

Keywords: Branch point signal sequences; Peanut; Intron; Molecular markers; Genetic diversity; Fingerprinting

Biochemical, Environmental, and Genetic Factors Associated with Paraoxonase (PON1) Activity by Jintana Sirivarasai; Sming Kaojarern; Thanyachai Sura; Krongtong Yoovathaworn (pp. 364-368).

A Novel Cationic Ribonuclease with Antimicrobial Activity from Rana dybowskii by Fengyun Tao; Meiyin Fan; Wei Zhao; Qiang Lin; Runyu Ma (pp. 369-384).

A novel ribonuclease (RNase) A superfamily gene (Rdronc) has been cloned from the frog Rana dybowskii. The deduced amino acid sequence shows that it belongs to the ribonuclease A superfamily, with the highest identity, 73%, to Rana pipiens onconase. Adaptive evolution analysis based on maximum likelihood models of codon substitution has been conducted on 10 members of the Rana RNases of subcluster B. Rapid adaptive evolution and multiple positive selection sites have been detected, which indicates that these genes may be evolving under positive selection pressure. Functional assay demonstrates that the recombinant Rdronc protein possesses antimicrobial activity against Gram-negative Escherichia coli and Pseudomonas aeruginosa and weaker antimicrobial activity against Gram-positive Staphylococcus aureus and yeast Candida albicans. Our findings support the hypothesis that ribonuclease A superfamily members may function in host defense of early-diversified vertebrates.

Keywords: Amphibian; Ribonuclease; Antimicrobial activity; Host defense; Positive selection

Polymorphism in the Prolactin Promoter and Its Association with Growth Traits in Chickens by T. K. Bhattacharya; R. N. Chatterjee; R. P. Sharma; M. Niranjan; U. Rajkumar; B. L. N. Reddy (pp. 385-394).

The pituitary hormone prolactin has a wide variety of functions involving growth, behavioral, and ovarian activities in chickens. The objectives of the present study were to identify polymorphisms in the prolactin promoter and estimate their effects on growth traits in White Leghorn chickens. Among 28 haplotypes found, the h1 haplotype was predominant. Body weight at 16 and 64 weeks and age at sexual maturity were significantly associated with haplotype combinations (P < 0.05). The h1/h1 haplogroup showed the highest body weight at 16 weeks of age, and h1/h7 was the highest at 64 weeks. The lowest age at sexual maturity was found in birds with the h1/h6 haplotype combination, and mRNA expression of prolactin was lowest in h1/h4 birds and highest in h1/h5 birds. The prolactin promoter was highly polymorphic and had significant associations with growth traits in White Leghorn chickens.

Keywords: Association; Chicken; Expression; Growth; Polymorphism; Prolactin promoter

Simulating Linkage Disequilibrium Structures in a Human Population for SNP Association Studies by Xiguo Yuan; Junying Zhang; Yue Wang (pp. 395-409).

Existing simulation methods usually simulate linkage disequilibrium (LD) structures starting with an initial population that is randomly generated according to specified allele frequencies. These at random based methods might be unstable because the LD level of the initial population is generally extremely low. This study presents a new algorithm, SIMLD, to simulate genome populations with real LD structures. SIMLD begins from an initial population with possibly the highest LD level, and then the LD decays to fit the desired level through processes of mating and recombination over generations. SIMLD can produce case–control samples according to various disease models. Using empirical SNP marker information from three populations of HapMap data, we implement the proposed algorithm and demonstrate a set of experimental results.

Keywords: Case–control; Disease models; Linkage disequilibrium; Simulation; SNPs

Identification and Mapping of a Novel Hydroxysafflor Yellow A (HSYA) Biosynthetic Gene in Carthamus tinctorius by Juan Yang; Yan Wang; Mei-Li Guo (pp. 410-415).

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Biochemical Genetics (v.49, #5-6)