Abstract. The Thorpe scale is an energy-containing vertical overturning scale of large eddies associated with sheargenerated turbulence. This study investigates indirect estimates of vertical diffusivities from the Thorpe scale method in the polar front region east of the Kerguelen Islands based on fine-scale density profiles gathered during the 2011 KEOPS2 (KErguelen Ocean and Plateau compared Study 2) cruise. These diffusivities are validated in comparison with diffusivities estimated from the turbulence dissipation rate directly measured via a TurboMAP (Turbulence ocean Microstructure Acquisition Profiler) microstructure profiler. The results are sensitive to the choice of the diffusivity parameterization and the overturn ratio R o , and the optimal results have been obtained from the parameterization by Shih et al. (2005) and the R o = 0.25 criterion, rather than the parameterization by Osborn (1980) and the R o = 0.2 criterion originally suggested by Gargett and Garner (2008).The Thorpe-scale-derived diffusivities in the KEOPS2 region show a high degree of spatial variability, ranging from a canonical value of O(10 −5 ) m 2 s −1 in the Winter Water layer and in the area immediately north of the polar front to a high value of O(10 −4 ) m 2 s −1 in the seasonal thermocline between the surface mixed layer and the Winter Water. The latter high diffusivities are found especially over the shallow plateau southeast of the Kerguelen Islands and along the polar front that is attached to the escarpment northeast of the islands. The interaction of strong frontal flow with prominent bottom topography likely causes the observed elevated mixing rates.

Manila clams, Ruditapes philippinarum, removed from their natural environment and maintained for 9 weeks in continuously immersed conditions exhibited a clear endogenous circatidal rhythm in oxygen consumption. The clams exhibited a semidiurnal rhythmicity in oxygen consumption after showing a diurnal pattern in the ®rst few days (5 to 7 d) of the experiment. The results of the present study indicate that activity rhythms of clams are controlled not only by exogenous factors, but also by an endogenous circatidal periodicity.

Genomic analysis of the hyperthermophilic archaeon Thermococcus onnurineus NA1 (TNA1) revealed the presence of a 471-bp open reading frame with 93% similarity to the dUTPase from Pyrococcus furiosus. The dUTPase-encoding gene was cloned and expressed in Escherichia coli. The purified protein hydrolyzed dUTP at about a 10-fold higher rate than dCTP. The protein behaved as a dimer in gel filtration chromatography, even though it contains five motifs that are conserved in all homotrimeric dUTPases. The dUTPase showed optimum activity at 80 degrees C and pH 8.0, and it was highly thermostable with a half-life (t (1/2)) of 170 min at 95 degrees C. The enzymatic activity of the dUTPase was largely unaffected by variations in MgCl(2), KCl, (NH(4))(2)SO(4), and Triton X-100 concentrations, although it was reduced by bovine serum albumin. Addition of the dUTPase to polymerase chain reactions (PCRs) run with TNA1 DNA polymerase significantly increased product yield, overcoming the inhibitory effect of dUTP. Further, addition of the dUTPase allowed PCR amplification of targets up to 15 kb in length using TNA1 DNA polymerase. This enzyme also improved the PCR efficiency of other archaeal family B type DNA polymerases, including Pfu and KOD.

Genomic analysis of a hyperthermophilic archaeon Thermococcus sp. NA1 revealed the presence of an 885-bp open reading frame encoding a protein of 295 amino acids with a calculated molecular mass of 32,981 Da. Analysis of the deduced amino acid sequence showed that amino acid residues important for catalytic activity and the metal binding ligands conserved in all of methionyl aminopeptidases (MetAP) were also conserved and belonged to type IIa MetAP. The protein, designated TNA1_MetAP (Thermococcus sp. NA1 MetAP), was cloned and expressed in Escherichia coli. The recombinant enzyme was a Mn(2+)-, Ni(2+)-, Fe(2+)-, or Co(2+)-dependent metallopeptidase. Optimal MetAP activity against L: -methionine p-nitroanilide (Met-pNA) (K (m) = 0.68 mM) occurred at pH 7.0 and 80 to 90 degrees C. The MetAP was very unstable compared to Pyrococcus furiosus MetAP, which was completely inactivated by heating at 80 degrees C for 5 min. It seemed likely that the cysteine residue (Cys53) played a critical role in regulating the thermostability of TNA1_MetAP.

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