Graffiti: graph-based classification in heterogeneous networks

We address the problem of multi-label classification in heterogeneous graphs, where nodes belong to different types and different types have different sets of classification labels. We present a novel approach that aims to classify nodes based on their neighborhoods. We model the mutual influence of nodes as a random walk in which the random surfer aims at distributing class labels to nodes while walking through the graph. When viewing class labels as “colors”, the random surfer is essentially spraying different node types with different color palettes; hence the name Graffiti of our method. In contrast to previous work on topic-based random surfer models, our approach captures and exploits the mutual influence of nodes of the same type based on their connections to nodes of other types. We show important properties of our algorithm such as convergence and scalability. We also confirm the practical viability of Graffiti by an experimental study on subsets of the popular social networks Flickr and LibraryThing. We demonstrate the superiority of our approach by comparing it to three other state-of-the-art techniques for graph-based classification.     

Double tagging recombinant A1- and A2A-adenosine receptors with hexahistidine and the FLAG epitope. Development of an efficient generic protein purification procedure

An expression plasmid for mammalian cells (CLDN10B) has been modified to add nucleotides encoding hexahistidine and the FLAG peptide (H/F) to cDNAs. The new mammalian expression plasmid has been named pDoubleTrouble (pDT). The plasmid and a recombinant baculovirus were used to produce native-and H/F-human A1 and A2A adenosine receptors, optimally expressed in CHO-K1 and Sf9 cells, respectively. Binding to recombinant H/F-A1 receptors (Bmax = 30 pmol/mg protein) was characterized using [3H]8-cyclopentyl-1,3-dipropylxanthine ([3H]CPX) and 125I-N6-aminobenzyladenosine (125I-ABA). Binding to H/F-A2A receptors (Bmax = 48 pmol/mg protein) was characterized using [3H]5'-N-ethylcarboxamidoadenosine ([3H]NECA) and [3H]2-[4-(2-carboxyethyl)phenethylamino]-NECA ([3H]CGS21680). By comparison to native receptors, the addition of H/F to the amino termini of these receptors had no effect on the binding affinities cyclic AMP accumulation in intact cells was not affected by the H/F extension. Anti-FLAG and Ni-nitrilotriacetic acid affinity chromatography resulted in high yield ( >50% overall recovery) of nearly homogeneous deglycosylation with N-glycosidase F. We anticipate that pDT will be generally useful for facilitating the purification in high yield of recombinant receptors and other proteins by single or sequential affinity chromatography steps.     

Membrane Melatonin Receptors Activated Cell Signaling in Physiology and Disease

The pineal hormone melatonin has attracted great scientific interest since its discovery in 1958. Despite the enormous number of basic and clinical studies the exact role of melatonin in respect to human physiology remains elusive. In humans, two high-affinity receptors for melatonin, MT1 and MT2, belonging to the family of G protein-coupled receptors (GPCRs) have been cloned and identified. The two receptor types activate Gi proteins and MT2 couples additionally to Gq proteins to modulate intracellular events. The individual effects of MT1 and MT2 receptor activation in a variety of cells are complemented by their ability to form homo- and heterodimers, the functional relevance of which is yet to be confirmed. Recently, several melatonin receptor genetic polymorphisms were discovered and implicated in pathology—for instance in type 2 diabetes, autoimmune disease, and cancer. The circadian patterns of melatonin secretion, its pleiotropic effects depending on cell type and condition, and the already demonstrated cross-talks of melatonin receptors with other signal transduction pathways further contribute to the perplexity of research on the role of the pineal hormone in humans. In this review we try to summarize the current knowledge on the membrane melatonin receptor activated cell signaling in physiology and pathology and their relevance to certain disease conditions including cancer.     

Technological properties of candidate probiotic Lactobacillus plantarum strains

The study of new probiotic strains for their technological relevance and use in dairy products is important for trade and industry. Eight Lactobacillus plantarum strains isolated from Bulgarian cheeses and selected for their potential probiotic properties were characterized. In vitro tests with the API ZYM system revealed high aminopeptidase and phosphatase activity, and weak lipolytic activity. The L. plantarum strains showed also a weak proteolytic activity and were characterized as slow variants on the base of their coagulation ability. They maintained high viability in fermented milk over extended shelf-times at refrigerated temperature and demonstrated a good adaptation to 6% NaCl. Among the preservatives, only calcium propionate did not affect the growth of L. plantarum. The highest concentrations used of potassium sorbate (0.5 and 1%) and nisaplin (0.02%) decreased the bacterial growth. One L. plantarum strain was tested as an adjunct to commercially available formula for cream cheese. This candidate probiotic culture withstood the technological processing and retained high number of 10⁷ cfu g^?1 at the end of the 3 months storage period at 4 °C.     

Artisanal cheeses relying on spontaneous fermentation as sources of unusual microbiota – The example of the Bulgarian ‘mehovo sirene’ skin bag cheese

The Bulgarian ‘mehovo sirene’ cheese is a type of regional artisanal cheese prepared from raw ewe milk in a skin bag relying on spontaneous fermentation. A metagenomics study revealed an unusual microbiome comprising beneficial bacteria such as Staphylococcus equorum, Lactococcus lactis, Streptococcus thermophilus, Lactobacillus delbrueckii, Lactobacillus kefiranofaciens, Lactococcus raffinolactis, Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Loigolactobacillus coryniformis. Our findings suggest that ‘mehovo sirene’ could have some functional food properties and is a source of beneficial microorganisms.