Synthesis of RNA containing O-beta-D-ribofuranosyl-(1'-2')-adenosine-5'-phosphate and 1-methyladenosine, minor components of tRNA

tRNA is best known for its function as amino acid carrier in the translation process, using the anticodon loop in the recognition process with mRNA. However, the impact of tRNA on cell function is much wider, and mutations in tRNA can lead to a broad range of diseases. Although the cloverleaf structure of tRNA is well-known based on X-ray-diffraction studies, little is known about the dynamics of this fold, the way structural dynamics of tRNA is influenced by the modified nucleotides present in tRNA, and their influence on the recognition of tRNA by synthetases, ribosomes, and other biomolecules. One of the reasons for this is the lack of good synthetic methods to incorporate modified nucleotides in tRNA so that larger amounts become available for NMR studies. Except of 2'-O-methylated nucleosides, only one other sugar-modified nucleoside is present in tRNA, i.e., 2'-O-beta-D-ribofuranosyl nucleosides. The T loop of tRNA often contains charged modified nucleosides, of which 1-methyladenosine and phosphorylated disaccharide nucleosides are striking examples. A protecting-group strategy was developed to introduce 1-methyladenosine and 5'-O-phosphorylated 2'-O-(beta-D-ribofuranosyl)-beta-D-ribofuranosyladenine in the same RNA fragment. The phosphorylation of the disaccharide nucleoside was performed after the assembly of the RNA on solid support. The modified RNA was characterized by mass-spectrometry analysis from the RNase T1 digestion fragments. The successful synthesis of this T loop of the tRNA of Schizosaccharomyces pombe initiator tRNA(Met) will be followed by its structural analysis by NMR and by studies on the influence of these modified nucleotides on dynamic interactions within the complete tRNA.     

Ecophysiological variabilities in ectohydrolytic enzyme activities of some Pseudoalteromonas species,P. citrea,P. issachenkonii,and P. nigrifaciens

The ecophysiological variabilities in the ectohydrolytic enzyme profiles of the three species of Pseudoalteromonas, P. citrea, P. issachenkonii, and P. nigrifaciens, have been investigated. Forty-one bacteria isolated from several invertebrates, macroalgae, sea grass, and the surrounding water exhibited different patterns of hydrolytic enzyme activities measured as the hydrolysis of either native biopolymers or fluorogenic substrates. The activities of the following enzymes were assayed: proteinase, tyrosinase, lipase, amylase, chitinase, agarase, fucoidan hydrolase, laminaranase, alginase, pustulanase, cellulase, beta-glucosidase, alpha- and beta-galactosidases, beta-N-acetylglucosaminidase, beta-glucosaminidase, beta-xylosidase, and alpha-mannosidase. The occurrence and cell-specific activities of all enzymes varied over a broad range (from 0 to 44 micromol EU per hour) and depended not only on taxonomic affiliation of the strain, but also on the source/place of its isolation. This suggests 'specialization' of different species for different types of polymeric substrates as, for example, all strains of P. citrea and P. issachenkonii hydrolyzed alginate and laminaran, while strains of P. nigrifaciens were lacking the ability to hydrolyze most of the algal polysaccharides. The incidence of certain enzymes such as fucoidan hydrolases, alginate lyases, agarases, and alpha-galactosidases might be strain specific and reflect its particular ecological habitat.     

Effect of spermine on interaction of DNA polymerase α from the loach (Misgurnus fossilis) eggs with DNA

Polyamines (putrescine, spermidine and spermine) cause a marked increase in the activity of the loach Misgurnus fossilis DNA polymerase α on activated (gapped) DNA. The stimulatory effect increases in the order: putrescine, spermidine, spermine. Kinetic analysis shows that spermine does not change the affinity of the polymerase for dTTP, but it decreases the enzyme affinity for DNA. The apparent K_m of the polymerase for activated DNA progressively increases from 14 to 1200 μM (nucleotide), if the concentration of spermine rises up to 2 mM, while V_max reaches a maximum at 0.5 mM spermine and then drops at higher polyamine concentrations. Native calf thymus DNA and especially single-stranded DNA from phage M13 appear to be inhibitors of α-polymerase activity on gapped DNA. Dixon plots suggest simple competitive inhibition of the polymerase activity by single- or double-stranded DNA and absence of cooperativity in the interaction of the polymerase with DNA. Hill-plot analysis is compatible with the interpretation that there is only one DNA binding site on each DNA polymerase α molecule. Spermine, even at low concentrations, decreases sharply the affinity of the enzyme for double-stranded DNA, while the enzyme affinity for single-stranded DNA changes insignificantly. Another result of spermine action is the destabilization of the polymerase-DNA complex. The ratio of the ‘static affinity’ of the enzyme to its ‘kinetic affinity’ decreases 2.2-fold in the presence of 0.5 mM spermine. As a result, the sensitivity of DNA synthesis to 3′-deoxy-3′-aminothymidine 5′-triphosphate and to 1-β-d-arabinofuranosylcytidine 5′-triphosphate decreases in the presence of the polyamine. Both spermine effects, the decrease in the ‘nonproductive binding’ of the polymerase to double-stranded regions in DNA and the destabilization of the polymerase-DNA complex, presumably account for the increase in the activity of the loach α-polymerase on activated DNA.     

13C multiplet nuclear magnetic resonance relaxation-derived ring puckering and backbone dynamics in proline-containing glycine-based peptides.

13CH2-multiplet nuclear magnetic resonance relaxation studies on proline (P)-containing glycine (G)-based peptides, GP, PG, GPG, PGG, and GPGG, provided numerous dipolar auto- and cross-correlation times for various motional model analyses of backbone and proline-ring bond rotations. Molecular dynamics simulations and bond rotation energy profiles were calculated to assess which motions could contribute most to observed relaxation phenomena. Results indicate that proline restricts backbone psi 1, psi 2, and phi 2 motions by 50% relative to those found for a polyglycine control peptide. psi 1 rotations are more restricted in the trans-proline isomer state than in the cis form. A two-state jump model best approximates proline ring puckering which in water could occur either by the C gamma endo-exo or by the C2 interconversion mechanism. The temperature dependence (5 degrees to 75 degrees C) of C beta, and C gamma, and C delta angular changes is rather flat, suggesting a near zero enthalpic contribution to the ring puckering process. In lower dielectric solvents, dimethylsulfoxide and methanol, which may mimic the hydrophobic environment within a protein, the endo-exo mechanism is preferred.     

Biogenic fluxes of carbon dioxide in the old-growth spruce forest in the middle taiga: Results of eddy covariance measurements

Fluxes of carbon dioxide in the old-growth bilberry spruce forest in the European Taiga are measured by the eddy covariance technique. A carbon dioxide sink to the ecosystem was observed from April until September; the maximum net-exchange rate of carbon dioxide was recorded in July. During the cold period of the year from October to March, the biogenic flux of CO₂ was directed from the forest canopy to the atmosphere. According to measurements at u* > 0.2, the total annual NEE was 219 g C m^–2; the annual values of the ecosystem respiration R _eco and the gross photosynthesis P _gross were 483 and 966 g C m^–2, respectively. The conclusion is that the old-growth bilberry spruce forest in the middle taiga subzone was the sink of carbon from the atmosphere during the year of observation.     

The peculiarities of polymorphism of XPD and XRCC1 repair genes in cells of down and Ehlers-Danlo syndrome patients characterized by increased radiosensitivity

Codon 312 and 751 polymorphisms of XPD gene and codon 399 polymorphism of XRCC1 gene of peripheral blood lymphocytes in patients with Down syndrome (DS) (46 individuals) and Ehlers-Danlo syndrome (EDS) (47 individuals) and in a group of healthy donors (control) (40 individuals) were studied. The frequency of XPD genotype (G312G) coding for the most effectively functioning form of XPD protein was lower in patients with DS (26%) than in the group of healthy donors (42.5%) (p = 0.035), whereas no significant differences with the control were revealed for this codon in patients with EDS. No patients with XPD genotype (C751C) (p = 0.036) were revealed in the group of EDS patients, while this genotype was found in 16% of the group of healthy donors and in 17% of patients with DS. A trend of XRCC1 genotype frequency reduction (A399A) (p = 0.085) in EDS patients (3.9%) compared with the group of healthy donors (13.5%) and DS patients (13.3%) was obtained. These data showed that polymorphisms of the excision repair genes under study were accompanied by an elevated individual radiosensitivity in patients with DS. Genes investigated (their polymorphic variants) did not participate in the mechanisms for radiosensitive phenotype formation in EDS patients.     

Live cell detection of caspase-3 activation by a Discosoma-red-fluorescent-protein-based fluorescence resonance energy transfer construct

A probe consisting of Discosoma red fluorescent protein (DsRed) and enhanced yellow fluorescent protein (EYFP) linked by a 19-amino-acid chain containing the caspase-3 cleavage site Asp-Glu-Val-Asp was developed to monitor caspase-3 activation in living cells. The expression of the tandem construct in mammalian cells yielded a strong red fluorescence when excited with 450- to 490-nm light or with a 488-nm argon ion laser line as a result of fluorescence resonance energy transfer (FRET) from donor EYFP to acceptor DsRed. The advantage over previous constructs using cyan fluorescent protein is that our construct can be used when excitation wavelengths lower than 488nm are not available. To validate the construct, murine HT-22 hippocampal neuronal cells were triggered to undergo CD95-induced neuronal death. An increase in caspase-3 activity was demonstrated by a reduction of FRET in cells transfected with the construct. This was manifested by a dequenching of EYFP fluorescence leading to an increase in EYFP emission and a corresponding decrease in DsRed fluorescence, which correlated with an increase in pro-caspase-3 processing. We conclude that CD95-induced caspase-3 activation in HT-22 cells was readily detected at the single-cell level using the DsRed-EYFP-based FRET construct, making this a useful technology to monitor caspase-3 activity in living cells.     

Effective anomerisation of 2'-deoxyadenosine derivatives during disaccharide nucleoside synthesis

The formation of a disaccharide nucleoside (11) by O3'-glycosylation of 5'-O-protected 2'-deoxyadenosine or its N6-benzoylated derivative has been observed to be accompanied by anomerisation to the corresponding alpha-anomeric product (12). The latter reaction can be explained by instability of the N-glycosidic bond of purine 2'-deoxynucleosides in the presence of Lewis acids. An independent study on the anomerisation of partly blocked 2'-deoxyadenosine has been carried out. Additionally, transglycosylation has been utilized in the synthesis of 3'-O-beta-D-ribofuranosyl-2'deoxyadenosines and its alpha-anomer.     

Neoclassical transport in stellarators without collisionless ion loss

For quasi-isodynamic stellarators with poloidally closed contours of the magnetic field strength and high plasma beta neoclassical transport coefficients are computationally obtained over a large range of mean free paths. In particular, a long-mean-free-path regime is found in which quasi-neutrality obtains without radial electric field.     

Double-strand breaks of DNA of C57BL and mdx mouse cardiomyocytes after dynamic stress

One of the approaches to analysis of survival of cardiomyocytes during oxidative stress can be the use of animals with genetic defects—mdx mice. In mdx mice, disturbance of dystrophine synthesis is known to be accompanied by development of oxydative stress in contractile cells that in turn produces cell death. Earlier we established that dynamic stress leads to the formation of low molecular DNA fragments in the mdx mouse myocardium. It is beyond any doubt that the DNA fragmentation develops via formation of double-strand DNA breaks (DB). To record the dynamics of the appearance and disappearance of DB in the mdx mouse cardiomyocytes after dynamic stress, we used an antibody to the phosphorylated form of the γ-H2Ax histone. In the absence of stress, DB in myocardial cell nuclei are revealed both in C57Bl and in mdx mice. The percentage of cardiomyocyte nuclei with DB in C57Bl and in mdx mice was 0.05 ± 0.07% and 6.7 ± 0.2%, respectively (Table 1). In the C57Bl mice 1 h after dynamic stress the fraction of labeled cardiomyocyte nuclei rose to 1.0 ± 0.02%, while in the mdx mice—to 41.7 ± 11.4% (Table 1). At 24 h after the dynamic stress 5.7 ± 0.2% cardiomyocyte nuclei remained labeled in the mdx mouse myocardium (Table 1), whereas in C57Bl mice no labeled cardiomyocyte nuclei were revealed. One hour after the dynamic stress, 0.3 ± 0.2% of cardiomyocyte nuclei of the C57Bl mice incorporated ³H-thymidine. In the mdx mice, 2.9 ± 0.5% of cardiomyocyte nuclei incorporated ³H-thymidine. At 24 h after the stress and ³H-thymidine administration the percentage of cardiomyocyte nuclei in the mdx mice fell to 0.4 ± 0.2%. In the C57Bl mice primarily labeled nuclei were not revealed. The ³H-thymidine incorporation is not associated with entrance of cardiomyocytes into the mitotic cycle; we consider it as a manifestation of reparative DNA synthesis. We conclude is that the disappearance of DB in DNA from the mdx mouse myocardium 24 h after the dynamic stress is associated both with DNA reparation and the loss of cardiomyocytes.