Recombination-deficient mutants of Salmonella typhimurium are avirulent and sensitive to the oxidative burst of macrophages

Mutations in the genes recA and recBC were constructed in the virulent Salmonella typhimurium strain 14028s. Both the recA and recBC mutants were attenuated in mice. The mutants were also sensitive to killing by macrophages in vitro. The recombination mutants were no longer macrophage sensitive in a variant line of J774 macrophage-like cells that fail to generate superoxide. This suggests that repair of DNA damage by Salmonella is necessary for full virulence in vivo and that the oxidative burst of phagocytes is one source of such DNA damage.     

Design considerations for two-stage enrichment clinical trials

When there is a predictive biomarker, enrichment can focus the clinical trial on a benefiting subpopulation. We describe a two-stage enrichment design, in which the first stage is designed to efficiently estimate a threshold and the second stage is a “phase III-like” trial on the enriched population. The goal of this paper is to explore design issues: sample size in Stages 1 and 2, and re-estimation of the Stage 2 sample size following Stage 1. By treating these as separate trials, we can gain insight into how the predictive nature of the biomarker specifically impacts the sample size. We also show that failure to adequately estimate the threshold can have disastrous consequences in the second stage. While any bivariate model could be used, we assume a continuous outcome and continuous biomarker, described by a bivariate normal model. The correlation coefficient between the outcome and biomarker is the key to understanding the behavior of the design, both for predictive and prognostic biomarkers. Through a series of simulations we illustrate the impact of model misspecification, consequences of poor threshold estimation, and requisite sample sizes that depend on the predictive nature of the biomarker. Such insight should be helpful in understanding and designing enrichment trials.     

Parthenogenesis in an elasmobranch in the presence of conspecific males

Parthenogenesis has been observed in several elasmobranch species, primarily in public aquaria. The majority of cases of parthenogenesis have occurred either when females were held without males or once a male was removed from a female's habitat. Here we report a second instance of parthenogenesis in a zebra shark female that was housed with conspecific mature males. This study calls into question the conditions under which elasmobranch females undergo parthenogenesis.     

Spatial components of foraging behavior in an African Ponerine ant,Paltothyreus tarsatus

Colonies of the African stink ant Paltothyreus tarsatuslocated in the forest have nests with shorter horizontal galleries and a smaller total foraging surface than colonies located in open areas. Each solitary worker specializes on the same central or peripheral hunting zone but she does not specialize on a particular sector during group-retrieving. The search for prey is characterized by a wandering walk with spatial parameters varying in two ways. Capture of a termite releases a path characterized by sinuosity and a decrease in speed of movement. In contrast, a failure in the course of an attempted capture releases an increase in both sinuosity and speed of movement corresponding to a socalled reserve behavior. Each worker shortens her retrieving trip in comparison with her search trip and the straightness of the homing paths depends on the size and shape of the prey. Our data show that behavioral flexibility at the individual level in P. tarsatusis important in determining spatial foraging strategy at the colony level.     

Characterization of the bioactive conformation of the C-terminal tripeptide Gly-Leu-Met-NH2 of substance P using [3-prolinoleucine10]SP analogues.

Residue Leu10 of substance P (SP) is critical for NK-1 receptor recognition and agonist activity. In order to probe the bioactive conformation of this residue, cis- and trans-3-substituted prolinoleucines were introduced in position 10 of SP. The substituted SP analogues were tested for their affinity to human NK-1 receptor specific binding sites (NK-1M and NK-1m) and their potency to stimulate adenylate cyclase and phospholipase C in CHO cells transfected with the human NK-1 receptor. [trans-3-prolinoleucine10]SP retained affinity and potency similar to SP whereas [cis-3-prolinoleucine10]SP shows dramatic loss of affinity and potency. To analyze the structural implications of these biological results, the conformational preferences of the SP analogues were analyzed by NMR spectroscopy and minimum-energy conformers of Ac-cis-3-prolinoleucine-NHMe, Ac-trans-3-prolinoleucine-NHMe and model dipeptides were generated by molecular mechanics calculations. From NMR and modeling studies it can be proposed that residue Leu10 of SP adopts a gauche(+) conformation around the chi1 angle and a trans conformation around the chi2 angle in the bioactive conformation. Together with previously published results, our data indicate that the C-terminal SP tripeptide should preferentially adopt an extended conformation or a PPII helical structure when bound to the receptor.     

Tyrosine protein kinase assays

Protein kinases form a large family of enzymes that play a major role in a number of live processes. The study of their action is important for the understanding of the transformation mechanisms and of the normal and pathological growth events. The quality of an enzyme assay is often the key point of an enzymatic study. It must be flexible and compatible with various experimental conditions, such as those for the purification process, the screening of inhibitors and the substrate specificity studies. As will be shown in the present review, two categories of substrates, peptidic and proteic, should be distinguished. The use of peptide substrates facilitates the determination of the recognition requirements of the enzyme and of the kinetic effects of even minute variations in their sequence. These linear peptide structures are assumed to mimic a complex interaction between the enzyme and a proteic substrate in which distant amino acids in the sequence are vicinal in the folded substrate. Less amenable to a systematic study, but probably more adequate to investigate the natural substrate of a given kinase, are the proteic substrates. Obviously the tools to measure protein kinase activities are not the same in these two cases. The main difficulty in assaying protein kinases is the use of labelles γ-ATP, mostly at large excess concentration, since the final product of the reaction has to be separated from the non-reacted labelled ATP. In the case of peptide substrates, the difficulty is to separate them from ATP basing on differences of molecular mass. Despite the efforts of many investigators to rely upon differences in solubility, in charges or in “affinity”, this separation, which is crucial for the assay, is still an unsolved experimental problem. Chromatographic, as well as electrophoretic assays appeared relatively late in this domain, and more work in assessing new methodologies might bring new breakthroughs in the next few years. Specific, simple and reliable kinase assays are still a major challenge. Their improvement will help to conduct specificity studies, to elucidate complex growth mechanisms in which they are involved and to discover more selective potent inihibitors.     

Aerolysin — the ins and outs of a model channel-forming toxin

Aerolysin is one of a large group of bacterial proteins that can kill target cells by forming discrete channels in their plasma membranes. The toxin has many properties in common with the porins of the Gram-negative bacterial outer membrane, including an extensive amount of β-structure, a high proportion of hydrophilic amino acid side-chains and no hydrophobic stretches in the primary structure. It also oligomerizes to produce an insertion-competent state. Aerolysin is secreted as a dimer by members of the Aeromonas family. It binds to a high-affinity receptor on the target cell that has recently been shown to be a glycosylphosphatidylinositol-anchored glycoprotein. Binding is followed by heptamerization to form a structure that we propose contains a β-barrel which can insert into the membrane and produce a channel.