Development of a multiplex allele-specific qPCR approach for testing PIK3CA mutations in patients with colorectal cancer.

Phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases involved in cellular growth and division. Somatic mutations in one of the PI3K catalytic subunit genes, PIK3CA, are frequently found in numerous malignancies, including colorectal cancer (CRC). Several PIK3CA inhibitors are approved for the treatment of breast cancer and lymphoma. Activating mutations in PIK3CA tend to occur in exons 9 and 20, with mutations in other exons 1, 4, and 7 being less common. Most test systems for PIK3CA mutation screening are designed to detect mutations in exons 9 and 20, leaving exons 1-7 overlooked. We have developed a multiplex AS-PCR to screen for PIK3CA mutations in exons 1, 4, 7, 9, and 20. Validation was performed on 515 CRC samples of patients from Siberia and the Far East of Russia. The assay sensitivity was 0.05-0.5% of mutant DNA, and the overall PIK3CA mutation frequency was 13.01%, with 9.32% of mutations in exon 9, 1.94% in exon 20, and 1.74% in exons 1-7. The assay designed is suitable for the analysis of activating PIK3CA mutations in formalin-fixed paraffin-embedded tissue samples. The present work is the first study characterizing the PIK3CA mutation frequency in CRC patients from the eastern part of Russia.

Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions.

At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity-the Peru-Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern-central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.

High Resistance of Resting Eggs of Cladoceran Moina macrocopa to the Effect of Heavy Metals.

The research aimed to determine critical concentrations of heavy metals at which survival of resting eggs of the cladoceran Moina macrocopa is negatively affected. Resting eggs' viability was not affected over a 30-days exposure towards copper, cadmium, zinc or nickel at concentrations up to 60-70 g/L. When resting eggs were exposed to sediment contaminated with heavy metals for 8 months, the hatching success was affected at 30 g copper/kg. Thus, resting eggs of Cladocera can tolerate heavy metals at concentrations that far exceed lethal concentrations of heavy metals to active life stage and exceed low or moderate levels of environmental pollution. Follow up investigation of life table parameters of hatchlings from resting eggs exposed to heavy metals demonstrated that neither lifespan nor fecundity of hatchlings differ from control animals. These results demonstrate that zooplankton may rapidly recover from resting egg bank once aquatic habitat becomes unpolluted.

Gamma irradiation of resting eggs of Moina macrocopa affects individual and population performance of hatchlings.

We investigated the effects of γ-radiation on the survival of resting eggs of the cladoceran Moina macrocopa, on the parameters of the life cycle of neonates hatched from the irradiated eggs and on the performance of the population initiated from irradiated eggs. The study showed that γ-radiation in a range of doses from the background level to 100 Gy had no effect on survival of irradiated eggs. The absorbed dose of 200 Gy was lethal to resting eggs of M. macrocopa. The number of clutches and net reproductive rate (R0) of hatchlings from eggs exposed to radiation were the strongly affected parameters in experiments with individual females. The number of clutches per female was drastically reduced for females hatched from egg exposed to 80-100 Gy. The most sensitive parameter was the R0. The estimated ED50 for the R0 (effective dose that induces 50% R0 reduction) was 50 Gy. Population performance was also affected by the irradiation of the resting stage of animals that initiated population. Populations that was initiated from hatchlings from resting eggs exposed to 100 Gy was of smaller size and with fewer juvenile and parthenogenetic females in comparison with control populations. Thus, we determined the dose-response relationship for the effect of gamma radiation on survival of resting eggs and individual and population responses of hatchlings from irradiated resting eggs. We conclude that for highly polluted areas contamination of bottom sediments with radioactive materials could affect zooplankton communities through adverse chronic effects on resting eggs, which will be transmitted to hatchlings at individual or population levels.

A replication study examining association of rs6983267, rs10090154, and rs1447295 common single nucleotide polymorphisms in 8q24 region with prostate cancer in Siberians.

INTRODUCTION: Multiple genetic studies have confirmed association of 8q24 variants with susceptibility to prostate cancer (CaP). However, the risk conferred in men living in Russia is unknown. MATERIALS AND METHODS: In this work we studied the association of rs6983267, rs10090154, and rs1447295 single nucleotide polymorphisms (SNPs) with a risk of CaP development in men of Caucasoid descent living in the Siberian region of Russia. Three 8q24 SNPs were genotyped by real-time polymerase chain reaction in histologically confirmed CaP "cases" (n = 392) and clinically evaluated "controls" (n = 344). To evaluate the SNP effects on CaP susceptibility, odds ratio (OR) and confidence interval (CI) 95% were calculated. Allele and genotype frequencies in the groups were compared using logistic regression; differences were considered statistically significant if P<0.05. RESULTS: We showed statistically significant association of the A allele of rs1447295 (OR [CI 95%] = 1.96 [1.37-2.81], P<0.0001) and the T allele of rs10090154 (OR [CI 95%] = 2.14 [1.41-3.26], P<0.0001) with CaP. The T-A rs10090154 to rs1447295 haplotype was also associated with CaP (OR [CI 95%] = 2.47 [1.59-3.85], P<0.0001). There was no significant association with the T allele of rs6983267: OR [CI 95%] = 0.9 [0.73-1.11], P> 0.05. CONCLUSION: Thus, our investigation confirms the role of chromosomal region 8q24 in the development of CaP in the Russian population.