Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus

Polymerases from the Pol-I family which are able to efficiently use ddNTPs have demonstrated a much improved performance when used to sequence DNA. A number of mutations have been made to the gene coding for the Pol-II family DNA polymerase from the archaeon Pyrococcus furiosus with the aim of improving ddNTP utilisation. ‘Rational’ alterations to amino acids likely to be near the dNTP binding site (based on sequence homologies and structural information) did not yield the desired level of selectivity for ddNTPs. However, alteration at four positions (Q472, A486, L490 and Y497) gave rise to variants which incorporated ddNTPs better than the wild type, allowing sequencing reactions to be carried out at lowered ddNTP:dNTP ratios. Wild-type Pfu–Pol required a ddNTP:dNTP ratio of 30:1; values of 5:1 (Q472H), 1:3 (L490W), 1:5 (A486Y) and 5:1 (Y497A) were found with the four mutants; A486Y representing a 150-fold improvement over the wild type. A486, L490 and Y497 are on an α-helix that lines the dNTP binding groove, but the side chains of the three amino acids point away from this groove; Q472 is in a loop that connects this α-helix to a second long helix. None of the four amino acids can contact the dNTP directly. Therefore, the increased selectivity for ddNTPs is likely to arise from two factors: (i) small overall changes in conformation that subtly alter the nucleotide triphosphate binding site such that ddNTPs become favoured; (ii) interference with a conformational change that may be critical both for the polymerisation step and discrimination between different nucleotide triphosphates.     

The mechanism of DNA repair by uracil-DNA glycosylase: studies using nucleotide analogues

2',4'-Dideoxy-4'-methyleneuridine incorporated into oligodeoxynucleotides forms regular B-DNA duplexes as shown by Tm and CD measurements. Such oligomers are not cleaved by the DNA repair enzyme, UDG, which cleaves the glycosylic bond in dU but not in dT nor in dC nucleosides in single stranded and double stranded DNA. Differential binding of oligomers containing carbadU, 4'-thiodU, and dU residues to wild type and mutant UDG proteins identify an essential role for the furanose 4'-oxygen in recognition and cleavage of dU residues in DNA.     

Triply triggered doxorubicin release from supramolecular nanocontainers

The synthesis of a supramolecular double hydrophilic block copolymer (DHBC) held together by cucurbit[8]uril (CB[8]) ternary complexation and its subsequent self-assembly into micelles is described. This system is responsive to multiple external triggers including temperature, pH and the addition of a competitive guest. The supramolecular block copolymer assembly consists of poly(N-isopropylacrylamide) (PNIPAAm) as a thermoresponsive block and poly(dimethylaminoethylmethacrylate) (PDMAEMA) as a pH-responsive block. Moreover, encapsulation and controlled drug release was demonstrated with this system using the chemotherapeutic drug doxorubicin (DOX). This triple stimuli-responsive DHBC micelle system represents an evolution over conventional double stimuli-responsive covalent diblock copolymer systems and displayed a significant reduction in the viability of HeLa cells upon triggered release of DOX from the supramolecular micellar nanocontainers.     

Efficient Single-Strand Break Repair Requires Binding to Both Poly(ADP-Ribose) and DNA by the Central BRCT Domain of XRCC1

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Effect of single-site charge-reversal mutations on the catalytic properties of yeast cytochrome c peroxidase: mutations near the high-affinity cytochrome c binding site

Fifteen single-site charge-reversal mutations of yeast cytochrome c peroxidase (CcP) have been constructed to determine the effect of localized charge on the catalytic properties of the enzyme. The mutations are located on the front face of CcP, near the cytochrome c binding site identified in the crystallographic structure of the yeast cytochrome c-CcP complex [Pelletier, H., and Kraut, J. (1992) Science 258, 1748-1755]. The mutants are characterized by absorption spectroscopy and hydrogen peroxide reactivity at both pH 6.0 and 7.5 and by steady-state kinetic studies using recombinant yeast iso-1-ferrocytochrome c(C102T) as a substrate at pH 7.5. Some of the charge-reversal mutations cause detectable changes in the absorption spectrum, especially at pH 7.5, reflecting changes in the equilibrium between penta- and hexacoordinate heme species in the enzyme. An increase in the amount of hexacoordinate heme in the mutant enzymes correlates with an increase in the fraction of enzyme that does not react with hydrogen peroxide. Steady-state velocity measurements indicate that five of the 15 mutations cause large increases in the Michaelis constant (R31E, D34K, D37K, E118K, and E290K). These data support the hypothesis that the cytochrome c-CcP complex observed in the crystal is the dominant catalytically active complex in solution.     

Adjustment of vibratory signals to ambient temperature in a host-searching parasitoid

Abstract.  Certain ichneumonid parasitoids (Hymenoptera) use self-produced vibrations transmitted on plant substrate, so-called vibrational sounding, to locate their immobile concealed pupal hosts. An ambient temperature dependency with higher frequencies and intensities at higher temperatures is postulated because signals are of myogenic origin. Here, temperature influence on vibratory signals is analysed in the temperate parasitoid Pimpla turionellae under different thermal conditions using plant-stem models to elicit host-searching behaviour. Signals are measured with laser Doppler vibrometry and analysed for time parameters and frequency components applying fast-Fourier transformations. The results reveal an unexpected effect of ambient temperature on signals produced by the female wasps. Although average values of time parameters (pulse trains, pulse train periods, inter pulse duration) are unchanged by ambient temperature, the frequency parameters show an inverse thermal effect. Within the temperature range tested (8–26 °C), decreasing temperature leads to significantly higher frequency and intensity of the self-produced vibrations in the temperate species. This inverse thermal effect may be explained by a temperature-coupled signal production in the frequency domain to compensate negative low-temperature effects on the mechanoreceptors by increased muscle activity. The option of heterothermy to produce signals reliably during vibrational sounding under low temperature is also discussed.     

Ontogeny of androgen and estrogen receptor expression in porcine testis: effect of reducing testicular estrogen synthesis

Reducing endogenous estrogen leads to increased proliferation of porcine Sertoli cells during the first 2 months of life. The resulting increase in porcine Sertoli cell numbers is maintained through puberty. The reduced estrogen appears to be the direct hormonal mediator because essentially no changes are observed in other hormones. However, the mechanism for this effect on Sertoli cell proliferation is unknown. The objective of these studies was to evaluate estrogen receptors alpha and beta (ESR1 and ESR2) in conjunction with androgen receptor (AR) on Sertoli cells and other testicular cell types, as an initial step toward understanding how reduced estrogen leads to increased Sertoli cell numbers. Testis sections from treated animals (aromatase inhibition to decrease endogenous estrogen beginning at 1 week of age) and from littermate controls treated with vehicle were subjected to immunocytochemical labeling for ESR1, ESR2, and AR. Three observers scored Sertoli cells, interstitial cells, peritubular myoid cells, and germ cells for intensity of labeling (0: absent; 1+: weak; 2+: moderate; or 3+: strong labeling). AR in Sertoli cells was readily detected at 1 week of age, was very faint in 2-month vehicle controls, and labeling appeared to increase in 3-month vehicle controls. AR in Sertoli cells, interstitial cells, and apparently germ cells was increased in treated animals at 2 months of age compared with the vehicle controls. This increase was confirmed in western blots. ESR1 and ESR 2 were clearly present in Sertoli cells from 1-week-old animals; ESR in Sertoli cells generally decreased with age with the decrease more apparent for ESR2. ESR1 in Sertoli cells and peritubular myoid cells exhibited some treatment-related effects but reduction of endogenous estrogen did not appear to affect ESR2 in the boar testis. The observed alterations in AR and ESR1 may mediate the increases in Sertoli cell proliferation following inhibition of endogenous estrogen production or may reflect the altered function of the Sertoli cells and peritubular myoid cells.     

Population dynamics of the threatened Oregon spotted frog before and after drought mitigation

Amphibians are among the most sensitive taxa to climate change, and species inhabiting arid and semiarid landscapes at the extremes of their range are especially vulnerable to drought. The Jack Creek, Oregon, USA, population of Oregon spotted frogs (Rana pretiosa) faces unique challenges because it occupies the highest elevation site in the species' extant range and one that has been transformed by loss of American beavers (Castor canadensis), which historically maintained open water. We evaluated the effects of drought mitigation (addition of excavated ponds) on relationships between local and regional water availability, inactive legacy beaver dams, and Oregon spotted frog population dynamics in the Jack Creek system. We conducted egg mass surveys and capture-mark-recapture sampling at a treatment reach with excavated ponds and 3 reference reaches over 13 years; surveys spanned a period before and after pond excavation at the treatment and 1 primary comparison reference reach. We analyzed data using a combination of robust design capture-mark-recapture estimators and generalized linear mixed models to characterize population dynamics. Adult Oregon spotted frog survival was approximately 19.5% higher at the treatment reach than the primary reference reach during the study period. Annual survival was most strongly associated with late summer vegetation greenness, a proxy for water availability, and males had higher survival than females. Among the 4 study reaches, the treatment reach consistently had higher late summer vegetation greenness, and the hydrology functioned more independently of regional precipitation patterns relative to the reference reaches; however, these dynamics were not linked to pond excavation. Breeding was concentrated in 2 legacy beaver ponds that were deepened by excavation during the study compared to an unexcavated beaver pond, 2 excavated ponds without legacy beaver dams, and 9 reference ponds. These results point to the benefit of enhancing existing beaver structures and indicate that management actions aimed at maintaining surface water for breeding in spring and saturated soils and ponded water for adults in late summer would benefit this unique population of Oregon spotted frogs in the face of drought.