A randomised, double-blind, controlled vaccine efficacy trial of DNA/MVA ME-TRAP against malaria infection in Gambian adults

Background

Many malaria vaccines are currently in development, although very few have been evaluated for efficacy in the field. Plasmodium falciparum multiple epitope (ME)– thrombospondin-related adhesion protein (TRAP) candidate vaccines are designed to potently induce effector T cells and so are a departure from earlier malaria vaccines evaluated in the field in terms of their mechanism of action. ME-TRAP vaccines encode a polyepitope string and the TRAP sporozoite antigen. Two vaccine vectors encoding ME-TRAP, plasmid DNA and modified vaccinia virus Ankara (MVA), when used sequentially in a prime-boost immunisation regime, induce high frequencies of effector T cells and partial protection, manifest as delay in time to parasitaemia, in a clinical challenge model.

Methods and Findings

A total of 372 Gambian men aged 15–45 y were randomised to receive either DNA ME-TRAP followed by MVA ME-TRAP or rabies vaccine (control). Of these men, 296 received three doses of vaccine timed to coincide with the beginning of the transmission season (141 in the DNA/MVA group and 155 in the rabies group) and were followed up. Volunteers were given sulphadoxine/pyrimethamine 2 wk before the final vaccination. Blood smears were collected weekly for 11 wk and whenever a volunteer developed symptoms compatible with malaria during the transmission season. The primary endpoint was time to first infection with asexual P. falciparum. Analysis was per protocol.DNA ME-TRAP and MVA ME-TRAP were safe and well-tolerated. Effector T cell responses to a non-vaccine strain of TRAP were 50-fold higher postvaccination in the malaria vaccine group than in the rabies vaccine group. Vaccine efficacy, adjusted for confounding factors, was 10.3% (95% confidence interval, −22% to +34%; p = 0.49). Incidence of malaria infection decreased with increasing age and was associated with ethnicity.

Conclusions

DNA/MVA heterologous prime-boost vaccination is safe and highly immunogenic for effector T cell induction in a malaria-endemic area. But despite having produced a substantial reduction in liver-stage parasites in challenge studies of non-immune volunteers, this first generation T cell–inducing vaccine was ineffective at reducing the natural infection rate in semi-immune African adults.     

The proliferation associated nuclear element (PANE1) is conserved between mammals and fish and preferentially expressed in activated lymphoid cells

The proliferation associated nuclear element (PANE1) had been identified in a screen for genes activated in mouse mammary epithelium transformed by stabilized beta-catenin. We have now cloned the human and zebrafish orthologs, analyzed their expression and expressed them ectopically in tissue culture cell lines. PANE1 consists of 180 amino acids and displays 38% conservation between man and zebrafish. Expression of the human PANE1 gene was detected preferentially in immune cells including leukemias and lymphomas, tumor tissues and tumor derived cell lines. In B- and T-cells PANE1 RNA was only detected after the respective cell types were activated either in vivo or in vitro.     

Use and optimization of a dual-flowrate loading strategy to maximize throughput in protein-a affinity chromatography

The effect of an alternate strategy employing two different flowrates during loading was explored as a means of increasing system productivity in Protein-A chromatography. The effect of such a loading strategy was evaluated using a chromatographic model that was able to accurately predict experimental breakthrough curves for this Protein-A system. A gradient-based optimization routine is carried out to establish the optimal loading conditions (initial and final flowrates and switching time). The two-step loading strategy (using a higher flowrate during the initial stages followed by a lower flowrate) was evaluated for an Fc-fusion protein and was found to result in significant improvements in process throughput. In an extension of this optimization routine, dynamic loading capacity and productivity were simultaneously optimized using a weighted objective function, and this result was compared to that obtained with the single flowrate. Again, the dual-flowrate strategy was found to be superior.     

Maximizing recovery of native protein from aggregates by optimizing pressure treatment

Recovering native protein from aggregates is a common obstacle in the production of recombinant proteins. Recent reports have shown that hydrostatic pressure is an attractive alternative to traditional denature-and-dilute techniques, both in terms of yield and process simplicity. To determine the effect of process variables, we subjected tailspike aggregates to a variety of pressure-treatment conditions. Maximum native tailspike yields were obtained with only short pressure incubations (<5 min) at 240 MPa. However, some tailspike aggregates were resistant to pressure, despite multiple cycles of pressure. Extending the postpressure incubation time to 4 days improved the yield of native protein from aggregates from 19.4 +/- 0.9 to 47.4 +/- 19.6 microg/mL (approximately 78% yield of native trimer from nonaggregate material). The nearly exclusive conversion of monomer to trimer over the time scale of days, when combined with previous kinetic data, allows for the identification of three postpressure kinetic phases: a rapid phase consisting of structured dimer conversion to trimer (30 min), an intermediate phase consisting of monomer conversion to aggregate (100 min), and a slow phase consisting of conversion of monomer to trimer (days). Optimizing the production of structured dimer can yield the highest level of folded protein. Typical refolding additives, such as glycerol, or low-temperature incubation did not improve yields.     

Effects of short-term chemical ablation of the GIP receptor on insulin secretion, islet morphology and glucose homeostasis in mice

Glucose-dependent insulinotropic polypeptide (GIP) is an incretin hormone secreted by endocrine K-cells in response to nutrient absorption. In this study we have utilized a specific and enzymatically stable GIP receptor antagonist, (Pro3)GIP, to evaluate the contribution of endogenous GIP to insulin secretion and glucose homeostasis in mice. Daily injection of (Pro3)GIP (25 nmol/kg body weight) for 11 days had no effect on food intake or body weight. Non-fasting plasma glucose concentrations were significantly raised (p<0.05) by day 11, while plasma insulin concentrations were not significantly different from saline treated controls. After 11 days, intraperitoneal glucose tolerance was significantly impaired in the (Pro3)GIP treated mice compared to control (p<0.01). Glucose-mediated insulin secretion was not significantly different between the two groups. Insulin sensitivity of 11-day (Pro3)GIP treated mice was slightly impaired 60 min post injection compared with controls. Following a 15 min refeeding period in 18 h fasted mice, food intake was not significantly different in (Pro3)GIP treated mice and controls. However, (Pro3)GIP treated mice displayed significantly elevated plasma glucose levels 30 and 60 min post feeding (p<0.05, in both cases). Postprandial insulin secretion was not significantly different and no changes in pancreatic insulin content or islet morphology were observed in (Pro3)GIP treated mice. The observed biological effects of (Pro3)GIP were reversed following cessation of treatment for 9 days. These data indicate that ablation of GIP signaling causes a readily reversible glucose intolerance without appreciable change of insulin secretion.     

Nonparametric estimation of the effects of quantitative trait loci

Interval mapping of quantitative trait loci from breeding experiments plays an important role in understanding the mechanisms of disease, both in humans and other organisms. Standard approaches to estimation involve parametric assumptions for the component distributions and may be sensitive to model misspecification. Some nonparametric tests have been studied. However, nonparametric estimation of the phenotypic distributions has not been considered in the genetics literature, even though such methods might provide essential nonparametric summaries for comparing different loci. We develop a sufficient condition for identifiability of the phenotypic distributions. Simple nonparametric estimators for the distributions are proposed for uncensored and right censored data. They have a closed form and their small and large sample properties are readily established. Their practical utility as numerical summaries which complement nonparametric tests is demonstrated on two recent genetics examples.     

Neutral and non-neutral macroecology

Because of the multiscalar nature of processes underlying biodiversity dynamics, macroecology has emerged as a discipline that seeks to build an understanding of this complexity by examining statistical patterns in large assemblages of species in geographic space and ecological time. Models that assume individual organisms within trophically defined assemblages are ecologically equivalent can produce many patterns identified by macroecology. Neutral models predict two important dynamical patterns that can be tested in real assemblages. First, they predict that species diversity will decline within an assemblage over time. The rate of this decay in species diversity can be predicted from estimates of migration rates from a “metacommunity” or species pool. Second, neutral models predict a divergence of species composition among local communities over time. The rate and degree of divergence among communities also depend on the migration rate. The few studies that have been done to date imply that the rate of migration in real species assemblages is much lower than that required to explain the degree of community similarity maintained in space and time. There are at least two alternative ways to extend neutral models to incorporate more biological realism. First, competitive asymmetries among species may be introduced to allow for the possibility that individuals of some species may have an advantage in replacing individuals that die. Second, environmental heterogeneity can be introduced by assuming sites available to individuals differ in quality to individuals of different species. The neutral model, because of its conceptual simplicity and rigor, should be considered as a null model for baseline comparison to actual patterns of distribution, abundance, species composition, and beta diversity.

Zusammenfassung

Wegen der multiskalaren Natur der Prozesse, die der Biodiversitätsdynamik zugrunde liegen, entstand die Makroökologie als eine Disziplin, die anstrebt ein Verständnis dieser Komplexität zu schaffen, indem sie statistische Muster in großen Vergesellschaftungen von Arten im geografischen Raum und ökologischer Zeit untersucht. Modelle, die davon ausgehen, dass individuelle Organismen innerhalb trophisch definierter Vergesellschaftungen ökologisch äquivalent sind, können viele Muster erzeugen, die durch die Makroökologie indentifiziert werden. Neutrale Modelle sagen zwei wichtige dynamische Muster vorher, die in realen Vergesellschaftungen getestet werden können. Als Erstes sagen sie vorher, dass die Artendiversität in einer Vergesellschaftung mit der Zeit abnehmen wird. Die Rate der Abnahme der Artendiversität kann über Schätzungen der Migrationsraten aus einer Metagemeinschaft bzw. einem Artenpool vorhergesagt werden. Als Zweites sagen neutrale Modelle eine Divergenz der Artenzusammensetzung zwischen den lokalen Gemeinschaften mit der Zeit vorher. Die Rate und der Grad der Divergenz zwischen den Gemeinschaften hängt ebenfalls von der Migrationsrate ab. Die wenigen Untersuchungen, die bis heute gemacht wurden, implizieren, dass die Rate der Migration in realen Artenvergesellschaftungen viel geringer als erforderlich sind, um den Grad der Gemeinschaftsähnlichkeit zu erklären, der in Raum und Zeit aufrecht erhalten wird. Es gibt mindestens zwei alternative Weisen neutrale Modelle zu erweitern, um mehr biologische Realität mit einzubeziehen. Als Erstes können Asymmetrien der Konkurrenz unter Arten einbezogen werden, um die Möglichkeit zu zulassen, dass Individuen einiger Arten einen Vorteil bei der Ersetzung von sterbenden Individuen haben. Als Zweites kann die Umweltheterogenität mit einbezogen werden, indem angenommen wird, dass sich die verfügbaren Standorte in ihrer Qualität für Individuen verschiedener Arten unterscheiden. Wegen seiner konzeptuellen Einfachheit und Starrheit sollte das neutrale Modell als Null-Modell für grundlegende Vergleiche von Verbreitung, Abundanz, Artenzusammensetzung und Betadiversität angesehen werden.     

FlyGEM, a full transcriptome array platform for the Drosophila community

We have constructed a DNA microarray to monitor expression of predicted genes in Drosophila. By using homotypic hybridizations, we show that the array performs reproducibly, that dye effects are minimal, and that array results agree with systematic northern blotting. The array gene list has been extensively annotated and linked-out to other databases. Incyte and the NIH have made the platform available to the community via academic microarray facilities selected by an NIH committee.