Transition-state stabilization by adenosine deaminase: structural studies of its inhibitory complex with deoxycoformycin

Experiments with radioactive deoxycoformycin indicate that the inhibitor is released from calf intestinal adenosine deaminase after the enzyme-inhibitor complex is disrupted by denaturation. Experiments with 2H2O and H218O indicate that the enzyme does not catalyze elimination-addition reactions that could have led to reversible covalent derivatization of the enzyme. Ultraviolet difference spectra and the influence of pH on inhibitor binding indicate that deoxycoformycin is bound intact as the neutral species, at a binding site that is less polar than solvent water. The enzyme-inhibitor complex appears to be held together by hydrogen bonds of extraordinary stability (ca. 10 kcal/mol). These results suggest that deamination proceeds by direct water attack, the enzyme acting as a general-base catalyst.     

Mentawai’s endemic,relictual fauna: is it evidence for Pleistocene extinctions on Sumatra?

Aim The four Mentawai islands, south‐west of Sumatra, have long been isolated from the remainder of Sundaland, resulting in a high level of endemism. We examined the distribution of 151 species of the Mentawai Islands in Sundaland and assessed various processes that may have resulted in the various biogeographical patterns. Location Southeast Asia, particularly the Mentawai Islands and nearby large landmasses (Sumatra, Java, Borneo and Peninsular Malaysia). Methods We compared the faunal composition of the Mentawai Islands for selected taxa (43 mammals, 92 reptiles and 16 amphibians) with that of the four nearby large landmasses of Sundaland using morphological comparisons and the most recent molecular phylogenetic analyses available in the literature. These comparisons yielded sister taxa, which were used to simulate species absence data for the four Sundaland landmasses under several scenarios to investigate how patterns of species absence could have arisen. Results In contrast to our expectations, several Mentawai species did not have their closest relatives on neighbouring Sumatra, but rather on the more distant Borneo, Java or Peninsular Malaysia. For mammals, the similarity between species from Mentawai and Borneo was greater than that observed between species from Mentawai and Sumatra. We conclude that the relationships represent traces of species historically distributed throughout Sundaland that became extinct in Sumatra during the Pleistocene. For reptiles and amphibians the observed pattern of species absences generally resembled the simulated pattern expected under the scenario of absence rates increasing with landmass isolation, whereas for mammals we observed more species than expected missing from Java and Sumatra, and fewer than expected from Borneo. Main conclusions The potential extinctions on Sumatra probably had two causes: changes of climate and vegetation during the Pleistocene and environmental impacts from the Toba supervolcanic eruption.     

Using occupancy models to investigate space partitioning between two sympatric large predators, the jaguar and puma in central Brazil

Coexistence of sympatric species is mediated by resource partitioning. Pumas occur sympatrically with jaguars throughout most of the jaguar's range but few studies have investigated space partitioning between both species. Here, camera trapping and occupancy models accounting for imperfect detection were employed in a Bayesian framework to investigate space partitioning between the jaguar and puma in Emas National Park (ENP), central Brazil. Jaguars were estimated to occupy 54.1% and pumas 39.3% of the sample sites. Jaguar occupancy was negatively correlated with distance to water and positively correlated with the amount of dense habitat surrounding the camera trap. Puma occupancy only showed a weak negative correlation with distance to water and with jaguar presence. Both species were less often present at the same site than expected under independent distributions. Jaguars had a significantly higher detection probability at cameras on roads than at off-road locations. For pumas, detection was similar on and off-road. Results indicate that both differences in habitat use and active avoidance shape space partitioning between jaguars and pumas in ENP. Considering its size, the jaguar is likely the competitively dominant of the two species. Owing to its habitat preferences, suitable jaguar habitat outside the park is probably sparse. Consequently, the jaguar population is likely largely confined to the park, while the puma population is known to extend into ENP's surroundings.     

The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities

Hepatitis C (HCV) protein 3/4A (NS3/4A) is a bifunctional enzyme comprising two separate domains with protease and helicase activities, which are essential for viral propagation. Both domains are stable and have enzymatic activity separately, and the relevance and implications of having protease and helicase together as a single protein remains to be explored. Altered in vitro activities of isolated domains compared with the full‐length NS3/4A protein suggest the existence of interdomain communication. The molecular mechanism and extent of this communication was investigated by probing the domain–domain interface observed in HCV NS3/4A crystal structures. We found in molecular dynamics simulations that the two domains of NS3/4A are dynamically coupled through the interface. Interestingly, mutations designed to disrupt this interface did not hinder the catalytic activities of either domain. In contrast, substrate cleavage and DNA unwinding by these mutants were mostly enhanced compared with the wild‐type protein. Disrupting the interface did not significantly alter RNA unwinding activity; however, the full‐length protein was more efficient in RNA unwinding than the isolated protease domain, suggesting a more direct role in RNA processing independent of the interface. Our findings suggest that HCV NS3/4A adopts an “extended” catalytically active conformation, and interface formation acts as a switch to regulate activity. We propose a unifying model connecting HCV NS3/4A conformational states and protease and helicase function, where interface formation and the dynamic interplay between the two enzymatic domains of HCV NS3/4A potentially modulate the protease and helicase activities in vivo.     

Interaction between growth hormone and insulin in the regulation of lipoprotein metabolism in the rat

The importance of insulin for the in vivo effects of growth hormone (GH) on lipid and lipoprotein metabolism was investigated by examining the effects of GH treatment of hypophysectomized (Hx) female rats with and without concomitant insulin treatment. Hypophysectomy-induced changes of HDL, apolipoprotein (apo)E, LDL, and apoB levels were normalized by GH treatment but not affected by insulin treatment. The hepatic triglyceride secretion rate was lower in Hx rats than in normal rats and increased by GH treatment. This effect of GH was blunted by insulin treatment. The triglyceride content in the liver changed in parallel with the changes in triglyceride secretion rate, indicating that the effect of the hormones on triglyceride secretion was dependent on changed availability of triglycerides for VLDL assembly. GH and insulin independently increased editing of apoB mRNA, but the effects were not additive. The expression of fatty-acid synthase (FAS), stearoyl-CoA desaturase-1 (SCD-1), and sterol regulatory element-binding protein-1c (SREBP-1c) was increased by GH treatment. Insulin and GH had no additive effects on these genes; instead, insulin blunted the effect of GH on SREBP-1c mRNA. In contrast to the liver, adipose tissue expression of SREBP-1c, FAS, or SCD-1 mRNA was not influenced by GH. In conclusion, the increased hepatic expression of lipogenic enzymes after GH treatment may be explained by increased expression of SREBP-1c. Insulin does not mediate the effects of GH but inhibits the stimulatory effect of GH on hepatic SREBP-1c expression and triglyceride secretion rate.     

Antibacterial activity of the contact and complement systems is blocked by SIC, a protein secreted by Streptococcus pyogenes

Recent studies have shown that activation of complement and contact systems results in the generation of antibacterial peptides. Streptococcus pyogenes, a major bacterial pathogen in humans, exists in >100 different serotypes due to sequence variation in the surface-associated M protein. Cases of invasive and life-threatening S. pyogenes infections are commonly associated with isolates of the M1 serotype, and in contrast to the large majority of M serotypes, M1 isolates all secrete the SIC protein. Here, we show that SIC interferes with the activation of the contact system and blocks the activity of antibacterial peptides generated through complement and contact activation. This effect promotes the growth of S. pyogenes in human plasma, and in a mouse model of S. pyogenes sepsis, SIC enhances bacterial dissemination, results which help explain the high frequency of severe S. pyogenes infections caused by isolates of the M1 serotype.     

Comparing Trials with Multiple Outcomes: The Multivariate One-Sided Hypothesis with Unknown Covariances

The paper deals with a problem arising for tests in clinical trials. The outcomes of a standard and a new treatment to be compared are multivariate normally distributed with common but unknown covariance matrix. Under the null hypothesis the means of the outcomes are equal, under the alternative the new treatment is assumed to be superior, i.e. the means are larger without further quantification. For known covariance matrix there is a variety of tests for this problem. Some of these procedures can be extended to the case of unknown covariances if one is willing to accept a bias. There is, however, also an efficient unbiased test. The paper contains some numerical comparisons of these different procedures and takes a look on the minimax properties of the unbiased test.