Journal of Applied Genetics

This study was conducted to detect polymorphisms in intron 1 of porcinePOU1F1 (POU domain, class 1, transcription factor1, Pit1, renamed asPOU1F1) by comparative sequencing. Within the intron, 23 sites of variation were identified, including 16 single-nucleotide substitutions, 4 single-nucleotide indels, 2 short (3-bp and 17-bp), and one long (313-bp) indels. Several important regulatory motifs were found within the 313-bp indel byin silico analysis. The 313-bp indel was next genotyped in 11 Chinese native pig breeds and 4 western meat-type pig breeds. The appearance of genotypes varied between breeds: among Chinese native breeds, no AA and AB genotypes were found in Tibetan, Lingao, Min, Rongchang, and Songliao Black pigs, no AA genotype was found in Fenjing and Leping Spotted pigs, whereas in Pietrain and Landrace there were no BB genotypes, and all 19 Duroc pigs were AA homozygotes. The western meat-type pigs had high A allele frequencies and the Chinese pigs had more B alleles, except Jianquhai pigs. A positive association of the AA genotype with birth weight was observed in a commercial pig line. This paper demonstrated that the genetic variation in intron 1 of the pigPOU1F1 gene was high and these polymorphisms may provide useful makers for QTL analysis.

The maintenance of genome integrity is essential for organism survival. Therefore, eukaryotic cells possess many DNA repair mechanisms in response to DNA damage. Acetyltransferase, Tip60, plays a central role in ATM and p53 activation which are involved in DNA repair. Recent works uncovered the roles of Tip60 in ATM and p53 activation and how Tip60 is recruited to double-strand break sites. Moreover, recent works have demonstrated the role of Tip60 in cancer progression. Here, we review the current understanding of how Tip60 activates both ATM and p53 in response to DNA damage and his new roles in tumorigenesis.

Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.

Genotypic variation in major components of the efficiency of nitrogen utilization and photosynthetic activity of flag leaves among old (released 1881–1963) and modern (released 1969–2003) cultivars of winter wheat was studied in field conditions under varied N fertilization levels (110, 90 and 80 kg N ha−1). Significant genotypic differences were observed for all characters. Their heritabilities ranged from 0.37 to 0.93 and were the lowest for the leaf efficiency of gas exchange, photosynthetic rate, straw N content and the economic index of N utilization efficiency (NUE). Some modern cultivars exhibited an enhanced tolerance to N shortage and several attributes of efficient N utilization (e.g. later senescing and more photosynthetically active flag leaves, increased ability to redistribute N into grains). The genotypes may serve as donors of appropriate characteristics for breeding. The observed cultivar-by-fertilization interactions suggest, however, that evaluations under diverse fertilization regimes may be necessary when searching for improved wheat efficiency and adaptation to less favourable environments.

Inheritance of partial leaf rust and stripe rust resistance of a Thatcher wheat 90RN2491, earlier reported to carry two doses of the gene pairLr34-Yr18 and the reference line RL6058 (6*Thatcher/PI58548) for theLr34-Yr18 gene pair was studied against predominant and highly virulent Indian races. Thatcher derivatives 90RN2491 and RL6058 were intercrossed as well as crossed with the leaf rust and stripe rust susceptible Indian cultivar WL711. The F1, F2 and F3 generations from these crosses were assessed for rust severity against leaf rust race 77-5 and stripe rust race 46S119. The F2 and F3 generations from the crosses of RL6058 and 90RN2491 with WL711, segregated 15 resistant : 1 susceptible (F2) and 7 homozygous resistant : 8 segregating : 1 homozygous susceptible (F3) ratios, respectively, both for leaf rust and stripe rust severity. Therefore, partial resistance against each of the leaf rust and stripe rust races in both RL6058 and 90RN2491 is ascribed to two independently inherited dominant genes. One of the two genes for leaf rust and stripe rust resistance in 90RN2491 and RL6058 isLr34 and the linked geneYr18, respectively. The second leaf rust resistance gene in both the Thatcher lines segregated independently of stripe rust resistance. Therefore, it is notLr34 and it remains unidentified.

The complete coding sequences of 3 porcine genes —ASPA, NAGA, andHEXA — were amplified by the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the mouse or other mammals and referenced pig ESTs. These 3 novel porcine genes were then deposited in the NCBI database and assigned GeneIDs: 100142661, 100142664 and 100142667. The phylogenetic tree analysis revealed that the porcineASPA, NAGA, andHEXA all have closer genetic relationships with theASPA, NAGA, andHEXA of cattle. Tissue expression profile analysis was also carried out and results revealed that swineASPA, NAGA, andHEXA genes were differentially expressed in various organs, including skeletal muscle, the heart, liver, fat, kidney, lung, and small and large intestines. Our experiment is the first one to establish the foundation for further research on these 3 swine genes.

The deregulation of Wnt signaling is observed in various cancers, including gliomas, and might be related to the methylation of the genes encoding antagonists of this signaling pathway. The aim of the study was to assess the methylation status of the promoter regions of six Wnt negative regulators and to determine their prognostic value in clinical samples of gliomas of different grades. The methylation of SFRP1, SFRP2, PPP2R2B, DKK1, SOX17, and DACH1 was analyzed in 64 glioma samples using methylation-specific polymerase chain reaction (MSP). The results were analyzed in correlation with clinicopathological data. Promoter methylation in at least one of the analyzed genes was found in 81.3 % of the tumors. All benign tumors [grade I according to the World Health Organization (WHO) classification] lacked the methylation of the studied genes, whereas grade II, III, and IV tumors were, in most cases, methylation-positive. The methylation index correlated with the patient’s age. The most frequently methylated genes were SFRP1 and SFRP2 (73.4 % and 46.9 %, respectively), followed by SOX17 (20.3 %) and PPP2R2B (10.9 %); DKK1 and DACH1 were basically unmethylated (1.6 %). SFRP1 methylation negatively correlated with patients’ survival time, and was significantly more frequent in older patients and those with higher grade tumors. Overall, the results of this study indicate that aberrant promoter methylation of Wnt pathway antagonists is common in gliomas, which may be the possible cause of up-regulation of this signaling pathway often observed in these tumors. Moreover, SFRP1 promoter methylation can be regarded as a potential indicator of glioma patients’ survival.

We screened a large group of primary ciliary dyskinesia/Kartagener syndrome (PCD/KS) patients and their siblings (148 patients from 126 unrelated families) for the presence of theCFTR mutations that are most frequently found in the Polish population: the severe F508del and 2,3del21kb, and the mild 3849+10kbC > T. No statistically significant increase in the frequency of these mutations was found in the studied group, as compared with the general population. This is consistent with an earlier observation in another population and indicates that the status of being a carrier of any of theseCFTR mutations should not be considered as an important risk factor in PCD/KS pathogenesis.