Searching for the Holy Grail; protein–protein interaction analysis and modulation

The first EMBO workshop on ‘Protein–Protein Interaction Analysis & Modulation’ took place in June 2012 in Roscoff, France. It brought together researchers to discuss the growing field of protein network analysis and the modulation of protein–protein interactions, as well as outstanding related issues including the daunting challenge of integrating interactomes in systems biology and in the modelling of signalling networks.     

Preliminary Evidence for the Amplification of Global Warming in Shallow,Intertidal Estuarine Waters

Over the past 50 years, mean annual water temperature in northeastern U.S. estuaries has increased by approximately 1.2°C, with most of the warming recorded in the winter and early spring. A recent survey and synthesis of data from four locations in Southern Rhode Island has led us to hypothesize that this warming may be amplified in the shallow (<1 m), nearshore portions of these estuaries. While intertidal areas are not typically selected as locations for long-term monitoring, we compiled data from published literature, theses, and reports that suggest that enhanced warming may be occurring, perhaps at rates three times higher than deeper estuarine waters. Warmer spring waters may be one of the factors influencing biota residing in intertidal regions both in general as well as at our specific sites. We observed greater abundance of fish, and size of Menidia sp., in recent (2010–2012) seine surveys compared to similar collections in 1962. While any linkages are speculative and data are preliminary, taken together they suggest that shallow intertidal portions of estuaries may be important places to look for the effects of climate change.     

Comparison of theoretical and experimental particle diffusion data within human airway casts

The dose delivered to airway cells is a critical factor whether one is addressing the therapeutic (i.e., positive) effects of inhaled pharmacologic agents or the toxic (i.e., negative) effects of pollutants. In this study, theoretical models describing particle deposition have been compared with experimental data from the literature. In the simulations, airways can be either roughor smooth-walled to be consistent with human lungs which can be either lined by cartilaginous rings (i.e., rough) or muscle (i.e., smooth). Particle motion for rough-walled airways within generations I=1–6 is calculated using the formula proposed by Martonen et al. (1). For smooth-walled airways within generations I=7–10, particle motion is calculated using the formula proposed by Martonen et al. (2). Theoretical predictions of particle deposition efficiencies are not only in agreement with the overall best fit empirical correlation presented by Cohen and Asgharian (3) over a wide range of dimensionless diffusion parameters, but also match individual experimental measurements (only available in I=1–6) with regard to effects of the parameters of particle size, flow rate, and airway dimensions. The mean difference in the ratio of experimental-to-theoretical particle diffusion values is 0.9 for a flow rate of 18 L/min and 1.1 for a flow rate of 34 L/min (i.e., the difference is only about 10%) within the upper airways of the casts (airway generations I=1–6), the mean difference for the whole casts was much greater. This may be attributed to the uncertainty of flow conditions in the peripheral airways as a result of the trimmmed nature of the casts. Overall, the findings suggest that the model can be a valuable component of aerosol therapy and risk assessment protocols, especially to address effects of enhanced deposition of pharmacologic drugs and radionuclides at sites within the human tracheobronchial tree.     

Amyloid Beta Precursor Protein and Prion Protein Have a Conserved Interaction Affecting Cell Adhesion and CNS Development

Genetic and biochemical mechanisms linking onset or progression of Alzheimer Disease and prion diseases have been lacking and/or controversial, and their etiologies are often considered independent. Here we document a novel, conserved and specific genetic interaction between the proteins that underlie these diseases, amyloid-β precursor protein and prion protein, APP and PRP, respectively. Knockdown of APP and/or PRNP homologs in the zebrafish (appa, appb, prp1, and prp2) produces a dose-dependent phenotype characterized by systemic morphological defects, reduced cell adhesion and CNS cell death. This genetic interaction is surprisingly exclusive in that prp1 genetically interacts with zebrafish appa, but not with appb, and the zebrafish paralog prp2 fails to interact with appa. Intriguingly, appa & appb are largely redundant in early zebrafish development yet their abilities to rescue CNS cell death are differentially contingent on prp1 abundance. Delivery of human APP or mouse Prnp mRNAs rescue the phenotypes observed in app-prp-depleted zebrafish, highlighting the conserved nature of this interaction. Immunoprecipitation revealed that human APP and PrP^C proteins can have a physical interaction. Our study reports a unique in vivo interdependence between APP and PRP loss-of-function, detailing a biochemical interaction that considerably expands the hypothesized roles of PRP in Alzheimer Disease.     

Antidepressants and advertising: psychopharmaceuticals in crisis

As the efficacy and science of psychopharmaceuticals has become increasingly uncertain, marketing of these drugs to both physicians and consumers continues to a central part of a multi-billion dollar per year industry in the United States. We explore how such drug marketing portrays idealized scientific relationships between psychopharmaceuticals and depression; how multiple stakeholders, including scientists, regulatory agencies, and patient advocacy groups, negotiate neurobiological explanations of mental illness; and how the placebo effect has become a critical issue in these debates, including the possible role of drug advertising to influence the placebo effect directly. We argue that if and how antidepressants "work" is not a straightforward objective question, but rather a larger social contest involving scientific debate, the political history of the pharmaceutical industry, cultural discourses surrounding the role of drugs in society, and the interpretive flexibility of personal experience.     

Herbivore-induced plant volatiles mediate host selection by a root herbivore

In response to herbivore attack, plants mobilize chemical defenses and release distinct bouquets of volatiles. Aboveground herbivores are known to use changes in leaf volatile patterns to make foraging decisions, but it remains unclear whether belowground herbivores also use volatiles to select suitable host plants. We therefore investigated how above- and belowground infestation affects the performance of the root feeder Diabrotica virgifera virgifera, and whether the larvae of this specialized beetle are able to use volatile cues to assess from a distance whether a potential host plant is already under herbivore attack. Diabrotica virgifera larvae showed stronger growth on roots previously attacked by conspecific larvae, but performed more poorly on roots of plants whose leaves had been attacked by larvae of the moth Spodoptera littoralis. Fittingly, D. virgifera larvae were attracted to plants that were infested with conspecifics, whereas they avoided plants that were attacked by S. littoralis. We identified (E)-β-caryophyllene, which is induced by D. virgifera, and ethylene, which is suppressed by S. littoralis, as two signals used by D. virgifera larvae to locate plants that are most suitable for their development. Our study demonstrates that soil-dwelling insects can use herbivore-induced changes in root volatile emissions to identify suitable host plants.     

Expression and purification of human tryptophan hydroxylase from Escherichia coli and Pichia pastoris

Tryptophan hydroxylase (TPH) from several mammalian species has previously been cloned and expressed in bacteria. However, due to the instability of wild type TPH, most successful attempts have been limited to the truncated forms of this enzyme. We have expressed full-length human TPH in large amounts in Escherichia coli and Pichia pastoris and purified the enzyme using new purification protocols. When expressed as a fusion protein in E. coli, the maltose-binding protein-TPH (MBP-TPH) fusion protein was more soluble than native TPH and the other fusion proteins and had a 3-fold higher specific activity than the His-Patch-thioredoxin-TPH and 6xHis-TPH fusion proteins. The purified MBP-TPH had a V(max) of 296 nmol/min/mg and a K(m) for L-tryptophan of 7.5+/-0.7 microM, compared to 18+/-5 microM for the partially purified enzyme from P. pastoris. To overcome the unfavorable properties of TPH, the stabilizing effect of different agents was investigated. Both tryptophan and glycerol had a stabilizing effect, whereas dithiothreitol, (6R)-5,6,7,8,-tetrahydrobiopterin, and Fe(2+) inactivated the enzyme. Irrespective of expression conditions, both native TPH expressed in bacteria or yeast, or TPH fusion proteins expressed in bacteria exhibited a strong tendency to aggregate and precipitate during purification, indicating that this is an intrinsic property of this enzyme. This supports previous observations that the enzyme in vivo may be stabilized by additional interactions.