ViLoN—a multi-layer network approach to data integration demonstrated for patient stratification

With more and more data being collected, modern network representations exploit the complementary nature of different data sources as well as similarities across patients. We here introduce the Variation of information fused Layers of Networks algorithm (ViLoN), a novel network-based approach for the integration of multiple molecular profiles. As a key innovation, it directly incorporates prior functional knowledge (KEGG, GO). In the constructed network of patients, patients are represented by networks of pathways, comprising genes that are linked by common functions and joint regulation in the disease. Patient stratification remains a key challenge both in the clinic and for research on disease mechanisms and treatments. We thus validated ViLoN for patient stratification on multiple data type combinations (gene expression, methylation, copy number), showing substantial improvements and consistently competitive performance for all. Notably, the incorporation of prior functional knowledge was critical for good results in the smaller cohorts (rectum adenocarcinoma: 90, esophageal carcinoma: 180), where alternative methods failed.     

Bacoside production by suspension cultures of Bacopa monnieri (L.) Pennell

Cell suspension cultures of Bacopa monnieri (L.) Pennell, grown in modified MS medium, grew some 5–6 fold over 40 days. Selected cell lines produced the important saponin, bacoside A, up to 1 g/100 g dry wt after this time.     

Activation of the p38 mitogen-activated protein kinase mediates the suppressive effects of type I interferons and transforming growth factor-beta on normal hematopoiesis.

Type I interferons (IFNs) are potent regulators of normal hematopoiesis in vitro and in vivo, but the mechanisms by which they suppress hematopoietic progenitor cell growth and differentiation are not known. In the present study we provide evidence that IFN alpha and IFN beta induce phosphorylation of the p38 mitogen-activated protein (Map) kinase in CD34+-derived primitive human hematopoietic progenitors. Such type I IFN-inducible phosphorylation of p38 results in activation of the catalytic domain of the kinase and sequential activation of the MAPK-activated protein kinase-2 (MapKapK-2 kinase), indicating the existence of a signaling cascade, activated downstream of p38 in hematopoietic progenitors. Our data indicate that activation of this signaling cascade by the type I IFN receptor is essential for the generation of the suppressive effects of type I IFNs on normal hematopoiesis. This is shown by studies demonstrating that pharmacological inhibitors of p38 reverse the growth inhibitory effects of IFN alpha and IFN beta on myeloid (colony-forming granulocytic-macrophage) and erythroid (burst-forming unit-erythroid) progenitor colony formation. In a similar manner, transforming growth factor beta, which also exhibits inhibitory effects on normal hematopoiesis, activates p38 and MapKapK-2 in human hematopoietic progenitors, whereas pharmacological inhibitors of p38 reverse its suppressive activities on both myeloid and erythroid colony formation. In further studies, we demonstrate that the primary mechanism by which the p38 Map kinase pathway mediates hematopoietic suppression is regulation of cell cycle progression and is unrelated to induction of apoptosis. Altogether, these findings establish that the p38 Map kinase pathway is a common effector for type I IFN and transforming growth factor beta signaling in human hematopoietic progenitors and plays a critical role in the induction of the suppressive effects of these cytokines on normal hematopoiesis.     

Allergenicity assessment of Allium sativum leaf agglutinin, a potential candidate protein for developing sap sucking insect resistant food crops

Background

Mannose-binding Allium sativum leaf agglutinin (ASAL) is highly antinutritional and toxic to various phloem-feeding hemipteran insects. ASAL has been expressed in a number of agriculturally important crops to develop resistance against those insects. Awareness of the safety aspect of ASAL is absolutely essential for developing ASAL transgenic plants.

Methodology/Principal Findings

Following the guidelines framed by the Food and Agriculture Organization/World Health Organization, the source of the gene, its sequence homology with potent allergens, clinical tests on mammalian systems, and the pepsin resistance and thermostability of the protein were considered to address the issue. No significant homology to the ASAL sequence was detected when compared to known allergenic proteins. The ELISA of blood sera collected from known allergy patients also failed to show significant evidence of cross-reactivity. In vitro and in vivo assays both indicated the digestibility of ASAL in the presence of pepsin in a minimum time period.

Conclusions/Significance

With these experiments, we concluded that ASAL does not possess any apparent features of an allergen. This is the first report regarding the monitoring of the allergenicity of any mannose-binding monocot lectin having insecticidal efficacy against hemipteran insects.     

TCR mimic monoclonal antibodies induce apoptosis of tumor cells via immune effector-independent mechanisms

mAbs that recognize peptides presented on the cell surface by MHC class I molecules are potential therapeutic agents for cancer therapy. We have previously demonstrated that these Abs, which we termed TCR mimic mAbs (TCRm), reduce tumor growth in models of breast carcinoma. However, mechanisms of TCRm-mediated tumor growth reduction remain largely unknown. In this study, we report that these Abs, in contrast to several mAbs used currently in the clinic, destroy tumor cells independently of immune effector mechanisms such as Ab-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). We found that TCRm-mediated apoptosis of tumor cells was associated with selective and specific binding of these Abs to peptide/HLA class I complexes, which triggered the activation of JNK and intrinsic caspase pathways. This signaling was accompanied by the release of mitochondrial cytochrome c and apoptosis-inducing factor. TCRm-induced apoptosis in tumor cells was completely inhibited by soluble MHC tetramers loaded with relevant peptide as well as with inhibitors for JNK and caspases. Furthermore, mAbs targeting MHC class I, independent of the peptide bound by HLA, did not stimulate apoptosis, suggesting that the Ab-binding site on the MHC/peptide complex determines cytotoxicity. This study suggests the existence of mechanisms, in addition to ADCC and CDC, through which these therapeutic Abs destroy tumor cells. These mechanisms would appear to be of particular importance in severely immunocompromised patients with advanced neoplastic disease, since immune cell-mediated killing of tumor cells through ADCC and CDC is substantially limited in these individuals.     

Morphology of the pharyngeal cavity, especially the surface ultrastructure of gill arches and gill rakers in relation to the feeding ecology of the catfish Rita rita (Siluriformes, Bagridae)

Gill arches and the gill rakers of a sluggish, carnivorous catfish, Rita rita, show significant differences of their surface ultrastructure, which are recognized adaptive modifications in relation to food and feeding ecology of fish. Gill rakers on the first and second pairs of gill arches are borne on the oral side and are long and stout at the epi-ceratobranchial union. Gill rakers on the third and fourth pairs of gill arches, in contrast, are borne on the oral and aboral sides and are relatively delicate and short. Long and stout gill rakers on the first and second pairs of gill arches are considered primarily to prevent entry of undesirably large food items into the pharynx. Two types of taste buds, Type I and Type II, occur on the gill arches and the gill rakers. The raised taste buds, located at the apical ends of the gill rakers on the third, fourth, and the fifth pairs of gill arches could increase gustatory efficiency in the pharynx. Differences in the distribution of taste buds on the pharyngeal sides of different gill arches indicate that the posterior part of the pharynx plays a more crucial role in gustation than does the anterior part. Co-occurrence of teeth and taste buds on the epi- and hypopharyngeal bones denotes that food processing and gustation occur simultaneously in the pharynx. Villiform and caniform teeth on the epi- and hypopharyngeal bones are associated with a complex food-processing cycle. Mucous secretions, oozing through mucous cell openings, provide lubrication facilitating smooth passage of food through the pharynx. The angle of curvature at the epi-ceratobranchial union of the first to fourth pairs of gill arches could assist the ventral drag of ceratobranchials in lowering of the pharyngeal floor, thus resulting in a great expansion of the pharynx, as needed to accommodate the large quantities of food captured.     

Enhanced photocatalytic activity of ceria-doped zinc oxide under UV illumination prepared via chemical precipitation

Transition metal oxide has emerged as one of the most potential candidates for environment remediation by utilizing solar energy through photocatalysis. This study compares the optical characteristics of zinc oxide (ZnO) and ceria-doped zinc oxide (CeZnO) nanoparticles synthesized through a facile chemical precipitation method without using any assistant catalyst. The present work investigates the consequences of ceria (cerium dioxide, CeO₂) intrusion on the photocatalytic activity of ZnO nanoparticles using methylene blue (MB) as a probe pollutant. The CeZnO showed an increase in photoactivity when compared to ZnO nanoparticles for degradation of MB in an aqueous solution under ultraviolet (UV) irradiance. The resulting heterojunction between ZnO and that of ceria enhances the charge separation efficiency showing a strong correlation between ZnO and CeO₂ heterojunction on the charge transfer mechanism across the interface.