Comparative analysis of N-acetylation polymorphism in humans as determined by phenotyping and genotyping

The N-acetylation polymorphisms of volunteers from the Moscow population analyzed by phenotyping and genotyping have been compared. The ratios between the proportions of fast acetylators (FAs) and slow acetylators (SAs) estimated by phenotyping and genotyping do not differ significantly from each other (47 and 44%, respectively). The absolute acetylation rate widely varies in both FAs and SAs. The NAT2 genotype and allele frequencies in the population sample have been calculated. The most frequent alleles are NAT2*4 (a "fast" allele), NAT2*5, and NAT2*6 ("slow" alleles); the most frequent genotypes are NAT2*5/*5, NAT2*4/*6, and NAT2*4/*5. Comparative analysis of N-acetylation polymorphism estimated by phenotyping and genotyping in the same subjects has shown a complete concordance between the phenotype and genotype in only 62 out of 75 subjects (87%). Comparative characteristics and presumed applications of the two approaches (quantitative estimation of acetylation rate and qualitative determination of the acetylator genotype) to the identification of individual acetylation status are presented.     

Soil‐nutrient availability under a global‐change scenario in a Mediterranean mountain ecosystem

Changes in rainfall availability will alter soil‐nutrient availability under a climate‐change scenario. However, studies have usually analyzed the effect of either drier or wetter soil conditions, despite the fact that both possibilities will coexist in many climatic regions of the world. Furthermore, its effect may vary across the different habitats of the ecosystem. We experimentally investigated the effect of three contrasting climatic scenarios on different carbon (C), nitrogen (N), and phosphorus (P) fractions in soil and microbial compartments among three characteristic habitats in a Mediterranean‐type ecosystem: forest, shrubland, and open areas. The climatic scenarios were dry summers, according to the 30% summer rainfall reduction projected in the Mediterranean; wet summer, simulating summer storms to reach the maximum historical records in the study area; and current climatic conditions (control). Sampling was replicated during two seasons (spring and summer) and 2 years. The climatic scenario did not affect the nutrient content in the litter layer. However, soil and microbial nutrients varied among seasons, habitats, and climatic scenarios. Soil‐nutrient fractions increased with lower soil‐moisture conditions (dry scenario and summer), whereas microbial nutrients increased under the wet summer scenario and spring. This pattern was consistent both studied years, although it was modulated by habitat, differences being lower with denser plant cover. Holm oak seedlings, used as live control of the experiment, tended to increase their N and P content (although not significantly) with water availability. Thus, the results support the idea that higher rainfall boosts microbial and plant‐nutrient uptake, and hence nutrient cycling. By contrast, a rainfall reduction leads to an accumulation of nutrients in the soil, increasing the risk of nutrient loss by leaching or erosion. These results show that the projected climate change will have significant effects on nutrient cycles, and therefore will have important implications on the ecosystem functioning.     

Biochip for determination of genetic markers of sporadic Alzheimer’s disease risk in the Russian Slavic population

A biological microchip (biochip) has been developed to study the genetic predisposition to sporadic form of Alzheimer’s disease (AD). The biochip allows of genotyping of ten genetic polymorphisms within APOE, TOMM40, APOJ, EXOC3L2, GAB2, A2M, CR1, BIN1, and PICALM genes. The assay includes the amplification of the loci of interest and subsequent allele-specific hybridization of the fluorescently labeled amplicons with oligonucleotides immobilized on the biochip. The genotyping of 166 patients and 128 controls revealed a significant association of APOE allele ?4 with susceptibility to AD (OR = 2.275, 95% CI 1.045–4.954, p = 0.034). Protective effects were observed for APOE allele ?2 and CLU (rs11136000) allele T (OR = 0.215, 59% CI 0.090–0.516, p = 0.001 and OR = 0.679, 95% CI 0.47–0.99, p = 0.042, respectively). A gene-gene interaction analysis revealed two AD-associated genotype combinations, APOE ?3/?4 GAB2 G/G (OR = 2.49, 95% CI 1.43–4.32, p = 0.001) and APOE ?4/?4 GAB2 G/G (OR = 3.55, 95% CI 1.23–10.24, p = 0.015). Based on the results of the combined multivariate analysis, an algorithm was developed to identify the individuals having a higher risk of AD.     

A new Late Jurassic turtle from Spain: phylogenetic implications,taphonomy and palaeoecology

Abstract: The Jurassic was an important period in the evolution of Testudinata and encompasses the origin of many clades, and this is especially true of Jurassic turtles from Western Europe. A new genus and species of Late Jurassic turtle, Hispaniachelys prebetica gen. et sp. nov. from the upper Oxfordian of the Prebetic (Southern Spain), is described on the basis of postcranial material. The specimen is the only known tetrapod from the Mesozoic of the Prebetic and the oldest turtle from southern Europe. A mosaic of characters indicates this is a new genus: it displays basal features including dorsal epiplastral processes/reduced cleithra, no medial contact of the extragulars and a long first thoracic rib, alongside derived characters including an absence of mesoplastra and the vertebral 3/4 sulcus crossing neural 5. The phylogenetic position of the new taxon is hard to resolve, and it might be either a paracryptodire or a basal testudine, but it is distinct from Plesiochelys. A complex taphonomic history is shown by a range of overlying grazing traces and bioerosion on the carapace. The carapace was subsequently overturned and buried ventrally up, terminating grazing activity, and was then bored by sponges before final burial. Scanning electron microscopy reveals phosphatic microspheroids associated with bacterial decay in the vascular cavities of the cancellous bone, suggesting the carapace may have acted as a closed microenvironment in which decay‐derived authigenic minerals formed.     

DOG-SPOT database for comprehensive management of dog genetic research data

Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides.     

Cyanine-dye-modified 2′-deoxyuridine-5′-triphosphates: Synthesis,applications, and linker effect on substrate properties for Taq DNA polymerase

A number of fluorescently labeled nucleoside triphosphates containing electroneutral indodicarbocyanine dye (Cy) have been synthesized. The dye has been attached to the C5 position of pyrimidine through the transalkene linkers of different structure. The synthesized labeled nucleoside triphosphates have been tested as substrates for Taq polymerase in PCR using the “TB-biochip” test system.     

The kinetics of fluorescent DNA labeling using PCR with different Taq polymerases depends on the chemical structures of modified nucleotides

The kinetics of DNA labeling during PCR using six fluorescent derivatives of 2′-deoxyuridine 5′-triphosphate has been studied. These compounds differ in their chemical structure, total electric charge and the length of the linker between a dye and the C5 position of a pyrimidine base. The efficiency of the incorporation of the fluorescent derivatives into a growing DNA chain by four commercially available Taq DNA polymerases with 5′→3′ exonuclease and hot start activity has been determined using real-time PCR with a TaqMan probe and the subsequent electrophoretic analysis of the reaction products. Modified deoxyuridines with a total positive or negative charge of the chromophore were practically not incorporated by Taq polymerases during PCR. The modified deoxyuridines with a neutral charge of the chromophore were effectively incorporated into DNA. The extended length of the linker between the pyrimidine base and the chromophore led to a lower PCR inhibition and a more effective inclusion of modified nucleotides in the growing DNA chain. This fact can be explained by the reduced steric effects that were caused by the dye. As a result, the most promising combinations of fluorescently labeled nucleotide and Taq polymerase have been chosen for further use in fluorescent DNA labeling.     

Association of polymophisms of renin-angiotensin and hemostasis system genes with ischemic stroke in Russians from central Russia

The allele and genotype frequencies of 14 SNPs of renin-angiotensin (REN, AGT, AGTR1, AGTR2, BKR2, and ADRB2) and hemostasis (FGB, F2, F5, F7, ITGB3, SERPINE1, MTHFR) system genes, as well as of the ACE insertion-deletion polymorphism, were analyzed in patients with ischemic stroke and in healthy controls matched by age, sex, and ethnicity. Genotyping was performed through the amplification of the selected gene sequences and subsequent hybridization of the labeled fragments with SNP-specific DNA probes on the biochip. There were no significant differences in the allele frequencies of individual genes between the groups of stroke patients and healthy donors. The contribution of the renin-angiotensin and hemostasis system genes to the genetic susceptibility to ischemic stroke in Russians from central Russia was also assessed using the MDR (Multifactor Dimensionality Reduction) approach. The genotype combination FGB G/- x ACE I/- x MTHFR C/- x SERPINE1 5G/5G, the frequency of which was significantly higher in patients with stroke than in healthy controls, was associated with an increased risk of ischemic stroke (P = 0.03, OR = 2.4, 95%CI 1.1?C5.3).     

Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides

Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.