In silico protein interaction analysis using the global proteome machine database

Experiments to probe for protein-protein interactions are the focus of functional proteomic studies, thus proteomic data repositories are increasingly likely to contain a large cross-section of such information. Here, we use the Global Proteome Machine database (GPMDB), which is the largest curated and publicly available proteomic data repository derived from tandem mass spectrometry, to develop an in silico protein interaction analysis tool. Using a human histone protein for method development, we positively identified an interaction partner from each histone protein family that forms the histone octameric complex. Moreover, this method, applied to the α subunits of the human proteasome, identified all of the subunits in the 20S core particle. Furthermore, we applied this approach to human integrin αIIb and integrin β3, a major receptor involved in the activation of platelets. We identified 28 proteins, including a protein network for integrin and platelet activation. In addition, proteins interacting with integrin β1 obtained using this method were validated by comparing them to those identified in a formaldehyde-supported coimmunoprecipitation experiment, protein-protein interaction databases and the literature. Our results demonstrate that in silico protein interaction analysis is a novel tool for identifying known/candidate protein-protein interactions and proteins with shared functions in a protein network.     

Identification of siRNA delivery enhancers by a chemical library screen

Most delivery systems for small interfering RNA therapeutics depend on endocytosis and release from endo-lysosomal compartments. One approach to improve delivery is to identify small molecules enhancing these steps. It is unclear to what extent such enhancers can be universally applied to different delivery systems and cell types. Here, we performed a compound library screen on two well-established siRNA delivery systems, lipid nanoparticles and cholesterol conjugated-siRNAs. We identified fifty-one enhancers improving gene silencing 2–5 fold. Strikingly, most enhancers displayed specificity for one delivery system only. By a combination of quantitative fluorescence and electron microscopy we found that the enhancers substantially differed in their mechanism of action, increasing either endocytic uptake or release of siRNAs from endosomes. Furthermore, they acted either on the delivery system itself or the cell, by modulating the endocytic system via distinct mechanisms. Interestingly, several compounds displayed activity on different cell types. As proof of principle, we showed that one compound enhanced siRNA delivery in primary endothelial cells in vitro and in the endocardium in the mouse heart. This study suggests that a pharmacological approach can improve the delivery of siRNAs in a system-specific fashion, by exploiting distinct mechanisms and acting upon multiple cell types.     

Two different types of dynorphin-A-immunoreactive terminals in rat substantia nigra

Summary The opioid peptide dynorphin A (1–17) is the third transmitter identified in the striatonigral projection, the other two being gamma-aminobutyric acid (GABA) and substance P. The ultrastructural features of the dynorphinergic terminals in substantia nigra/pars reticulata were studied using pre-embedding immunocytochemistry with the classical peroxidase-antiperoxidase-diaminobenzidine-method; these features were compared with GABAergic boutons visualized with an immunogold method. Two distinct types of dynorphin-A-immunoreactive boutons could be identified: (1) type A (81%) possessing characteristics similar to the GA-BAergic nerve endings in this region, i.e., large pleomorphic vesicles and symmetric synaptic contacts, (2) type B (19%) displaying asymmetric synaptic zones and small, mostly round vesicles. These results are in agreement with physiological studies suggesting a dual action of dynorphin A in substantia nigra.     

Sequential SDF1a and b-induced mobility guides Medaka PGC migration

Assembly and formation of the gonad primordium are the first steps toward gonad differentiation and subsequent sex differentiation. Primordial germ cells (PGCs) give rise to the gametes that are responsible for the development of a new organism in the next generation. In many organisms, following their specification the germ cells migrate toward the location of the prospective gonadal primordium. To accomplish this, the PGCs obtain directional cues from cells positioned along their migration path. One such cue, the chemokine SDF1 (stromal cell-derived factor 1) and its receptor CXCR4 have recently been found to be critical for proper PGC migration in zebrafish, chick and mouse.We have studied the mechanisms responsible for PGC migration in Medaka. In contrast to the situation observed in zebrafish, where proper PGC positioning is the result of active migration in the direction of the source of SDF1a, Medaka PGC movements are shown to be the consequence of a combination of active SDF1a and SDF1b-guided migration. In this process both SDF1 co-orthologues show only partly overlapping expression pattern and cooperate in the correct positioning of the PGCs.     

Phage display screening for peptidic chitinase inhibitors

A phage display library with disulfide-cyclized peptides was screened for peptides binding to chitinases from Serratia marcescens. One of those peptides was found to efficiently inhibit chitinase A and two others were inhibitors of chitinase B. Complete substitutional analysis of all three peptides using cellulose-bound peptide spot synthesis revealed key interaction positions and allowed optimization of the chitinase B inhibitory peptides towards higher affinity, with inhibitory constants in the lower nanomolar range. Inhibition by all peptides proved to be competitive and highly specific for the chitinase used to select them, as shown with a series of chitinases from different organisms.     

Phosphorylation of the yeast γ-tubulin Tub4 regulates microtubule function

The yeast γ-tubulin Tub4 is assembled with Spc97 and Spc98 into the small Tub4 complex. The Tub4 complex binds via the receptor proteins Spc72 and Spc110 to the spindle pole body (SPB), the functional equivalent of the mammalian centrosome, where the Tub4 complex organizes cytoplasmic and nuclear microtubules. Little is known about the regulation of the Tub4 complex. Here, we isolated the Tub4 complex with the bound receptors from yeast cells. Analysis of the purified Tub4 complex by mass spectrometry identified more than 50 phosphorylation sites in Spc72, Spc97, Spc98, Spc110 and Tub4. To examine the functional relevance of the phosphorylation sites, phospho-mimicking and non-phosphorylatable mutations in Tub4, Spc97 and Spc98 were analyzed. Three phosphorylation sites in Tub4 were found to be critical for Tub4 stability and microtubule organization. One of the sites is highly conserved in γ-tubulins from yeast to human.     

Improved sulfur nutrition provides the basis for enhanced production of sulfur-containing defense compounds in Arabidopsis thaliana upon inoculation with Alternaria brassicicola

The antifungal activities of many sulfur-containing defense compounds suggest a connection between pathogen infection, primary sulfur metabolism and sulfate nutritional status of plants. This relationship was investigated using Arabidopsis thaliana plants that were cultivated under different sulfur regimes and challenged by Alternaria brassicicola. Plants grown with 500 μM sulfate were significantly less infected compared to plants grown on 50 μM sulfate. Upon infection, the formation of the sulfur-containing defense compound camalexin and the gene expression of the sulfur-rich defense peptide defensin were clearly enhanced in plants grown with an optimal compared to a sufficient sulfate supply in the growth medium. Elevated levels of sulfite and O-acetylserine and cysteine biosynthetic enzymes after infection indicated a stimulation of sulfur metabolism under the higher sulfate supply. The results suggest that, in addition to pathogen-triggered activation of sulfur metabolism and sulfur-containing defense compound formation, the sulfate nutritional status is sensed to contribute to plant defense.     

Intrasexual and intersexual dimorphisms of the red salmon prosencephalon

Intrasexual as well as intersexual dimorphisms were found in the prosencephalon and mesencephalon of adult Oncorhynchus nerka (red/sockeye salmon). These dimorphisms are concerned with the position of the preoptic nucleus, nucleus lateralis tuberis, habenula, third ventricle, tectal ventricles, preoptic recess, recessus lateralis, horizontal commissure, posterior commissure, and toral commissure. The intrasexual dimorphism was characterized by either a rostral ("r"-pattern) or a caudal ("c"-pattern) position of the preoptic region as well as varying locations of other structures within the prosencephalon. As compared to "c"-pattern fish, the preoptic nucleus and nucleus lateralis tuberis were located more rostral, and the habenula was positioned further caudal, in "r"-type animals. The intersexual dimorphism was also characterized by different positions of the structures listed above. With the exception of the preoptic nucleus, all of these were located further rostral in "r"-pattern females than in type "r" males. In "c"-pattern females, they were positioned further caudal than in type "c" males. The number of neurons in the parvocellular and in the magnocellular portion of the preoptic region differed in the two genders with respect to "r"- as well as "c"-pattern fish. Males had more neurons than females in both the magno- and the parvocellular subdivisions of the preoptic region. In "r"- and "c"-pattern fish, the average size of magnocellular preoptic neurons was larger in females than in males. The observed intersexual variations may reflect gender-specific differences in the control of the pituitary. Functional correlates of intrasexual dimorphism are obscure.