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.     

Edging along a Warming Coast: A Range Extension for a Common Sandy Beach Crab

Determining the position of range edges is the first step in developing an understanding of the ecological and evolutionary dynamics in play as species’ ranges shift in response to climate change. Here, we study the leading (poleward) range edge of Ocypode cordimanus, a ghost crab that is common along the central to northern east coast of Australia. Our study establishes the poleward range edge of adults of this species to be at Merimbula (36.90°S, 149.93°E), 270 km (along the coast) south of the previous southernmost museum record. We also establish that dispersal of pelagic larvae results in recruitment to beaches 248 km (along the coast; 0.9° of latitude) beyond the adult range edge we have documented here. Although we cannot conclusively demonstrate that the leading range edge for this species has moved polewards in response to climate change, this range edge does fall within a “hotspot” of ocean warming, where surface isotherms are moving southwards along the coast at 20–50 km.decade^-1; coastal air temperatures in the region are also warming. If these patterns persist, future range extensions could be anticipated. On the basis of their ecology, allied with their occupancy of ocean beaches, which are home to taxa that are particularly amenable to climate-change studies, we propose that ghost crabs like O. cordimanus represent ideal model organisms with which to study ecological and evolutionary processes associated with climate change. The fact that “hotspots” of ocean warming on four other continents correspond with poleward range edges of ghost crab species suggests that results of hypothesis tests could be generalized, yielding excellent opportunities to rapidly progress knowledge in this field.     

OLETF (Otsuka Long-Evans Tokushima Fatty) rats that lack the CCK 1 (A) receptor develop less behavioral sensitization to repeated cocaine treatment than wild type LETO (Long Evans Tokushima Otsuka) rats.

OLETF (Otsuka Long-Evans Tokushima Fatty) lacking the CCK 1 (A) receptor have similar spontaneous activity and locomotor response (horizontal and vertical activity) in response to a single injection of cocaine as the wild type LETO (Long Evans Tokushima Otsuka) rats. In contrast, the OLETF rats display more stereotypy in response to the first dose of cocaine than the LETO rats. Tested at 7 and 14 days after a one week daily treatment with cocaine, the LETO rats display robust behavioral sensitization to cocaine while the OLETF rats did not. These results support the hypothesis that endogenous CCK released by cocaine treatment and acting at CCK 1 receptors is required for the development and/or expression of this behavior.     

Characterization and antimicrobial activity of 4-(β-D-glucopyranosyl-1→4-α-L-rhamnopyranosyloxy)-benzyl thiocarboxamide; a novel bioactive compound from Moringa oleifera seed extract

Antimicrobial activity of crude seed extract of Moringa oleifera was investigated by thin layer chromatography bioassay against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Cladosporium cladosporioides, and Penicillium sclerotigenum; most of them were prominently inhibited by an isolate with R _F 0.92–0.96. Characterization and identification of the extract revealed the occurrence of three bioactive compounds: 4-(α-l-rhamnopyranosyloxy)benzyl isothiocyanate, methyl N-4-(α-l-rhamnopyranosyloxy) benzyl carbamate (both known compounds), and 4-(β-d-glucopyranosyl-1→4-α-l-rhamnopyranosyloxy)-benzyl thiocarboxamide, existence of which in any Moringa spp. or plant is reported for the first time. The UV spectrum of the novel compound showed maximum absorption at 273 and 225 nm in MeOH while the IR spectrum revealed several characteristic bands at 3100, 2900, 1700, 1500, 1300, 1100 and 1000 cm⁻¹. The ¹H-NMR showed signals at 1.2 and 3.77 ppm and the ¹³C-NMR presented signals at 155, 122, 91.7 and 98.4 ppm. All the compounds at 5 mg/L had very high bactericidal activity against some of test pathogens even at contact period 1–2 h. 4-(β-d-Glucopyranosyl-1→4-α-l-rhamnopyranosyloxy)benzyl thiocarboxamide was the most potent, with 99.2 % inhibition toward Shigella dysenteriae and 100 % toward Bacillus cereus, E. coli and Salmonella typhi within 4 h of contact.     

Artificial waterway design affects fish assemblages in urban estuaries

Fishes were collected from residential canal estates leading directly off natural estuaries and artificial lakes with control tidal exchange in south-east Queensland, Australia, to test the model that the difference in artificial waterway design affects fish assemblages. A total of 17 779 fish representing 52 species was caught, including 23 species of economic importance (45% of the catch). Total fish abundance and species richness differed little among sites within or between the two artificial habitats (canals and lakes) in either of the seasons sampled (winter and spring). Multivariate analysis showed, however, that assemblages differed among sites within the same artificial habitat. The differences were best explained by the distance sites were from open water, while salinity, water temperature and dissolved oxygen explained little of the variability. Most species were found in canals and lakes, but there were enough differences in composition between the habitats to detect a difference in both seasons (significant ANOSIM tests). Salinity was lower in lakes because of the tidal restrictions, and while this was only weakly correlated with differences in fish assemblages, it had the most explanatory power of any environmental variable. New recruits arrived later in lakes than canals, perhaps because of the barriers to tidal flow. A survey the following year showed that differences among individual lakes were consistent through time, offering insights into the influence of different tidal barriers on fish assemblages. The design change from canals to lakes has a minor influence on fish assemblages and alters the timing of recruitment.     

IL-10 Signaling Blockade Controls Murine West Nile Virus Infection

West Nile virus (WNV), a mosquito-borne single-stranded RNA flavivirus, can cause significant human morbidity and mortality. Our data show that interleukin-10 (IL-10) is dramatically elevated both in vitro and in vivo following WNV infection. Consistent with an etiologic role of IL-10 in WNV pathogenesis, we find that WNV infection is markedly diminished in IL-10 deficient (IL-10^−/−) mice, and pharmacologic blockade of IL-10 signaling by IL-10 neutralizing antibody increases survival of WNV-infected mice. Increased production of antiviral cytokines in IL-10^−/− mice is associated with more efficient control of WNV infection. Moreover, CD4⁺ T cells produce copious amounts of IL-10, and may be an important cellular source of IL-10 during WNV infection in vivo. In conclusion, IL-10 signaling plays a negative role in immunity against WNV infection, and blockade of IL-10 signaling by genetic or pharmacologic means helps to control viral infection, suggesting a novel anti-WNV therapeutic strategy.     

Solution structure of alpha t alpha, a helical hairpin peptide of de novo design.

alpha t alpha is a 38-residue peptide designed to adopt a helical hairpin conformation in solution (Fezoui Y, Weaver DL Osterhout JJ, 1995, Protein Sci 4:286-295). A previous study of the carboxylate form of alpha t alpha by CD and two-dimensional NMR indicated that the peptide was highly helical and that the helices associated in approximately the intended orientation (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675-3679). Here, the solution structure of alpha t alpha as determined by two-dimensional NMR is reported. A total of 266 experimentally derived distance restraints and 20 dihedral angle restraints derived from J-couplings were used. One-hundred initial structures were generated by distance geometry and refined by dynamical simulated annealing. Twenty-three of the lowest-energy structures consistent with the experimental restraints were analyzed. The results presented here show that alpha t alpha is comprised of two associating helices connected by a turn region.