Evolutionary impact of human Alu repetitive elements

Early studies of human Alu retrotransposons focused on their origin, evolution and biological properties, but current focus is shifting toward the effect of Alu elements on evolution of the human genome. Recent analyses indicate that numerous factors have affected the chromosomal distribution of Alu elements over time, including male-driven insertions, deletions and rapid CpG mutations after their retrotransposition. Unequal crossing over between Alu elements can lead to local mutations or to large segmental duplications responsible for genetic diseases and long-term evolutionary changes. Alu elements can also affect human (primate) evolution by introducing alternative splice sites in existing genes. Studying the Alu family in a human genomic context is likely to have general significance for our understanding of the evolutionary impact of other repetitive elements in diverse eukaryotic genomes.     

H2O2 and Src-dependent transactivation of the EGF receptor mediates the stimulatory effect of leptin on renal ERK and Na+, K+-ATPase

We examined the mechanism through which leptin increases Na⁺, K⁺-ATPase activity in the rat kidney. Leptin was infused under anaesthesia into the abdominal aorta proximally to the renal arteries and then Na⁺, K⁺-ATPase activity was measured in the renal cortex and medulla. Leptin (1 μg/kg min) increased Na⁺, K⁺-ATPase activity after 3 h of infusion, which was accompanied by the increase in urinary H₂O₂ excretion and phosphorylation level of extracellular signal regulated kinase (ERK). The effect of leptin on ERK and Na⁺, K⁺-ATPase was abolished by catalase, specific inhibitors of epidermal growth factor (EGF) receptor, AG1478 and PD158780, as well as by ERK inhibitor, PD98059, and was mimicked by both exogenous H₂O₂ and EGF. The effect of leptin was also prevented by the inhibitor of Src tyrosine kinase, PP2. Leptin and H₂O₂ increased Src phosphorylation at Tyr⁴¹⁸. We conclude that leptin-induced stimulation of renal Na⁺, K⁺-ATPase involves H₂O₂ generation, Src kinase, transactivation of the EGF receptor, and stimulation of ERK.     

Charges of phosphate groups. A role in stabilization of 2'-deoxyribonucleotides. A DFT investigation

We have analyzed the relative stabilities and Gibbs tautomeric free energy for tautomeric transitions of neutral 2'-deoxyribonucleotides and its mono- and di-protonated forms. Geometry optimizations of these nucleic acid constituents have been performed at the DFT/B3LYP level using the standard 6-31G(d) basis set. The prediction of relative stabilities, Gibbs tautomeric free energy has been made at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level of theory. For each nucleoside four major conformers, i.e., north/anti, north/syn, south/anti, and south/syn have been taken into consideration. We have found the substantial effect of the uncompensated charge on the relative stability of 2'-deoxyribonucleotides. In particular, when the charge of 2'-deoxyribonucleotide anions is completely compensated by protons, the syn conformations have been found to be the global minima due to stabilization provided by intramolecular hydrogen bonds. However, the negative charge that appears due to the successive removal of the protons from the phosphate group destabilizes these syn conformations and stabilizes preferably the south/anti conformations (except of 2'-deoxyguanosine phosphate). Only 2'-deoxyribonucleotides, possessing south/anti and north/anti orientations, containing guanine and cytosine can contribute significantly to the rate of spontaneous point mutations due to the formation of biologically relevant amounts of 'rare' tautomers. However, we found strong influence of uncompensated negative charge for 2'-deoxyribonucleotides which possess syn conformations. Finally we have found that the proton transfer could result in the spontaneous change of 2'-deoxyribonucleotides conformations. We conclude that this phenomenon could be considered as a new way for the stabilization of 'rare' isomers for such DNA bases as cytosine and thymine.     

Solvent effects on fluorescence properties of protochlorophyll and its derivatives with various porphyrin side chains

Fluorescence spectra and fluorescence lifetimes of protochlorophyll (Pchl) were measured in organic solvents having different physical and chemical properties and were analyzed taking into account the nonspecific (dependent on bulk solvent parameters), and specific (e.g. H bonds, Mg coordination) solvent–solute interactions. The energy of the fluorescence emission band decreased, while the Stokes shift increased for increasing solvent orientation polarizability, which is a function of both the dielectric constant (ε) and the refractive index (n). The extent of the dependence of the Stokes shift on solvent orientation polarizability was higher in protic (i.e. those able to form hydrogen-binding) than in aprotic solvents. High value of the Stokes shift was also observed in pyridine and methanol, i.e. in solvents hexacoordinating the central Mg atom. The fluorescence decay of Pchl was monoexponential in all of the investigated solvents. The fluorescence lifetime decreased for increasing solvent orientation polarizability from 5.5 ± 0.1 ns in 1,4-dioxane to 3.3 ± 0.1 ns in methanol. Longer lifetime values were observed in the case of aprotic solvents than in protic solvents. The hexacoordination of Mg had no effect on the fluorescence lifetime. The present data are discussed with respect to results found for protochlorophyllide (Pchlide) (My?liwa-Kurdziel et al. in Photochem Photobiol 79:62–67, 2004), and they indicate that the presence of phytol chain in the porphyrin ring influences the spectral properties of the whole chromophore. This is the first complex analysis comparing the fluorescence emission and fluorescence lifetimes of purified Pchl and Pchlide.     

Application of STS markers for leaf rust resistance genes in near-isogenic lines of spring wheat cv. Thatcher

Sequence tagged site (STS) markers for eight resistance genes against Puccinia recondita f. sp. tritici were used to screen a set of near-isogenic lines of wheat cv. Thatcher containing in total 40 different Lr genes and their alleles. Polymerase chain reaction (PCR) analysis was carried out by using STS, SCAR and CAPS primers specific for the leaf rust resistance genes Lr1, Lr9, Lr10, Lr19, Lr24, Lr28, Lr37 and Lr47. The STS, CAPS and SCAR markers linked to resistance genes Lr9, Lr10, Lr19, Lr24, Lr37 and Lr47 were found to be reliable in diverse genetic backgrounds. The amplification product of the Lr1 gene marker was detected in the susceptible cv. Thatcher and in all of the near-isogenic lines examined except Lr2a, Lr2b, Lr2c and Lr19. The sequence analysis of PCR products amplified in lines Lr1, Lr10, Lr28 and in cv. Thatcher indicated that the near-isogenic lines and cv. Thatcher contained in the targeted chromosome region an allele that differed from the original alleles corresponding to Lr1/6*Thatcher (TLR621) and susceptible Thatcher (TH621). The amplification product specific to the STS marker of the Lr1 gene was amplified in almost all Thatcher near-isogenic lines and in cv. Thatcher because their alleles possessed primer sequences identical to the original allele TLR621. The marker for the Lr28 resistance gene was identified in line Lr28, carrying gene Lr28, and in 21 other near-isogenic lines. The sequencing of PCR products specific to Lr28 and generated in lines Lr1, Lr10 and Lr28 indicated that the lines Lr1, Lr10 and Lr28 are heterozygous in this region.     

Fasting-induced inhibition of collagen biosynthesis in rat skin. A possible role for phosphoenolpyruvate in this process

Fasting is accompanied by a decrease in collagen biosynthesis. The mechanism of this phenomenon involves inhibition of prolidase activity, an enzyme that plays a key role in upregulation of collagen metabolism. The mechanism of fasting-induced inhibition of prolidase activity is not known. Phosphoenolpyruvate (PEP) is known as a strong inhibitor of prolidase activity. It exerts this effect by inhibition of the enzyme phosphorylation. Unphosphorylated prolidase is inactive. One may expect that fasting-associated increase in posphoenolpyruvate content in animal tissues may be a factor which inactivates prolidase and makes it inactive in collagen biosynthesis. We measured the levels of phosphoenolpyruvate, pyruvate, and pyruvate kinase in the skin of control and fasted rats and correlated these parameters with prolidase expression, prolidase activity and collagen biosynthesis in this tissue. Significant increase of PEP concentration (about 30%) was found in the skin of fasted rats. In the same time prolidase activity and collagen biosynthesis decreased by about 50% and 30%, respectively, compared to controls. It is known that phosphoenolpyruvate is converted to pyruvate by the action of pyruvate kinase. Since fasting significantly decreases the activity of this enzyme, one may suggest that the accumulation of PEP is caused by a reduced utilisation of this metabolite. As demonstrated by Western immunoblot analysis the decrease in prolidase activity was not accompanied by a decrease in the amount of the enzyme protein. Instead, a decrease in the enzyme phosphorylation was observed. The reduction in phosphorylation seems to be responsible for the decrease in prolidase activity. These data suggest that fasting-evoked accumulation of PEP reduces the activity of prolidase, providing a mechanism for inhibition of collagen biosynthesis in the skin.     

Validity of the Indicator Organism Paradigm for Pathogen Reduction in Reclaimed Water and Public Health Protection

The validity of using indicator organisms (total and fecal coliforms, enterococci, Clostridium perfringens, and F-specific coliphages) to predict the presence or absence of pathogens (infectious enteric viruses, Cryptosporidium, and Giardia) was tested at six wastewater reclamation facilities. Multiple samplings conducted at each facility over a 1-year period. Larger sample volumes for indicators (0.2 to 0.4 liters) and pathogens (30 to 100 liters) resulted in more sensitive detection limits than are typical of routine monitoring. Microorganisms were detected in disinfected effluent samples at the following frequencies: total coliforms, 63%; fecal coliforms, 27%; enterococci, 27%; C. perfringens, 61%; F-specific coliphages, ~40%; and enteric viruses, 31%. Cryptosporidium oocysts and Giardia cysts were detected in 70% and 80%, respectively, of reclaimed water samples. Viable Cryptosporidium, based on cell culture infectivity assays, was detected in 20% of the reclaimed water samples. No strong correlation was found for any indicator-pathogen combination. When data for all indicators were tested using discriminant analysis, the presence/absence patterns for Giardia cysts, Cryptosporidium oocysts, infectious Cryptosporidium, and infectious enteric viruses were predicted for over 71% of disinfected effluents. The failure of measurements of single indicator organism to correlate with pathogens suggests that public health is not adequately protected by simple monitoring schemes based on detection of a single indicator, particularly at the detection limits routinely employed. Monitoring a suite of indicator organisms in reclaimed effluent is more likely to be predictive of the presence of certain pathogens, and a need for additional pathogen monitoring in reclaimed water in order to protect public health is suggested by this study.     

Testosterone Increases Susceptibility to Amebic Liver Abscess in Mice and Mediates Inhibition of IFNγ Secretion in Natural Killer T Cells

Amebic liver abscess (ALA), a parasitic disease due to infection with the protozoan Entamoeba histolytica, occurs age and gender dependent with strong preferences for adult males. Using a mouse model for ALA with a similar male bias for the disease, we have investigated the role of female and male sexual hormones and provide evidence for a strong contribution of testosterone. Removal of testosterone by orchiectomy significantly reduced sizes of abscesses in male mice, while substitution of testosterone increased development of ALA in female mice. Activation of natural killer T (NKT) cells, which are known to be important for the control of ALA, is influenced by testosterone. Specifically activated NKT cells isolated from female mice produce more IFNγ compared to NKT cells derived from male mice. This high level production of IFNγ in female derived NKT cells was inhibited by testosterone substitution, while the IFNγ production in male derived NKT cells was increased by orchiectomy. Gender dependent differences were not a result of differences in the total number of NKT cells, but a result of a higher activation potential for the CD4⁻ NKT cell subpopulation in female mice. Taken together, we conclude that the hormone status of the host, in particular the testosterone level, determines susceptibility to ALA at least in a mouse model of the disease.     

Uranium and thorium in muscle tissue of fish taken from the southern Baltic

The determination of U and Th was carried out on pooled samples of muscle tissue of cod (Gadus morhua), herring (Clupea harengus), sprat (Sprattus sprattus) and some other species of fish caught in 1981 in the southern Baltic. The levels of U obtained in the present study are generally within the ranges presented by other authors for fish from different aquatic regions of the world. The concentrations of U are similar to those found for Th in Baltic fish analysed. The concentration factors CF_U(Th), discrimination factors DF_U/Th and Th/U ratios (by weight) were calculated and discussed. These coefficients were also compared with values determined in other Baltic organisms. Transfer of U and Th along a food chain from potential prey (diet) to fish as predator (consumer) was quantified with a transfer factor.