Prediction of protein hydration sites from sequence by modular neural networks

The hydration properties of a protein are important determinants of its structure and function. Here, modular neural networks are employed to predict ordered hydration sites using protein sequence information. First, secondary structure and solvent accessibility are predicted from sequence with two separate neural networks. These predictions are used as input together with protein sequences for networks predicting hydration of residues, backbone atoms and sidechains. These networks are trained with protein crystal structures. The prediction of hydration is improved by adding information on secondary structure and solvent accessibility and, using actual values of these properties, residue hydration can be predicted to 77% accuracy with a Matthews coefficient of 0.43. However, predicted property data with an accuracy of 60-70% result in less than half the improvement in predictive performance observed using the actual values. The inclusion of property information allows a smaller sequence window to be used in the networks to predict hydration. It has a greater impact on the accuracy of hydration site prediction for backbone atoms than for sidechains and for non-polar than polar residues. The networks provide insight into the mutual interdependencies between the location of ordered water sites and the structural and chemical characteristics of the protein residues.      

Priming of blood neutrophils in children with cystic fibrosis: correlation between functional and phenotypic expression of opsonin receptors before and after platelet-activating factor priming

Ovine interferon-tau (ovIFN-tau) is a pregnancy recognition hormone required for normal embryonic development in sheep. In addition to its novel role in reproductive physiology, ovIFN-tau displays antiviral and antiproliferative activities similar to the IFN-alpha subtypes. To probe the structural basis for its unique activity profile, the crystal structure of ovIFN-tau has been determined at 2.1 A resolution. The fold of ovIFN-tau is similar to the previously determined crystal structures of human IFN-alpha2b and human and murine IFN-beta, which each contain five alpha-helices. Comparison of ovIFN-tau with huIFN-alpha2b, huIFN-beta, and muIFN-beta reveals unexpected structural differences that occur in regions of considerable sequence identity. Specifically, main-chain differences up to 11 A occur for residues in helix A, the AB loop, helix B, and the BC loop. Furthermore, these regions are known to be important for receptor binding and biological activity. Of particular interest, a buried ion pair is observed in ovIFN-tau between Glu71 and Arg145 which displaces a conserved tryptophan residue (Trp77) from the helical bundle core. This ion pair represents a major change in the core of ovIFN-tau compared to huIFN-alpha2b. Based on amino acid sequence comparisons, these ovIFN-tau structural features may be conserved in several human IFN-alpha subtypes and IFN-omega. The structure identifies potential problems in interpreting site-directed mutagenesis data on the human IFN-alpha family that consists of 12 proteins.     

Cell proliferation,viability, and in vitro differentiation of equine mesenchymal stem cells seeded on bacterial cellulose hydrogel scaffolds

The culture of multipotent mesenchymal stem cells on natural biopolymers holds great promise for treatments of connective tissue disorders such as osteoarthritis. The safety and performance of such therapies relies on the systematic in vitro evaluation of the developed stem cell-biomaterial constructs prior to in vivo implantation. This study evaluates bacterial cellulose (BC), a biocompatible natural polymer, as a scaffold for equine-derived bone marrow mesenchymal stem cells (EqMSCs) for application in bone and cartilage tissue engineering. An equine model was chosen due to similarities in size, load and types of joint injuries suffered by horses and humans. Lyophilized and critical point dried BC hydrogel scaffolds were characterized using scanning electron microscopy (SEM) to confirm nanostructure morphology which demonstrated that critical point drying induces fibre bundling unlike lyophilisation. EqMSCs positively expressed the undifferentiated pluripotent mesenchymal stem cell surface markers CD44 and CD90. The BC scaffolds were shown to be cytocompatible, supporting cellular adhesion and proliferation, and allowed for osteogenic and chondrogenic differentiation of EqMSCs. The cells seeded on the BC hydrogel were shown to be viable and metabolically active. These findings demonstrate that the combination of a BC hydrogel and EqMSCs are promising constructs for musculoskeletal tissue engineering applications.     

Unusual cutaneous infectious and parasitic diseases

The cutaneous manifestations of thirteen unusual infections and parasitic diseases are described. Their geographic distribution, morphologic features of the causative organism, histopathologic changes, criteria for diagnosis, and treatment are included.     

Effect of crosslink density on fracture behavior of model epoxies containing block copolymer nanoparticles

Model diglycidyl ether of bisphenol-A based epoxy resins containing well-dispersed 15 nm block copolymer (BCP) nanoparticles were prepared to study the effect of matrix crosslink density on their fracture behavior. The crosslink density of the model epoxies was varied via the controlled epoxy thermoset technology and estimated experimentally. As expected, it was found that the fracture toughness of the BCP-toughened epoxy is strongly influenced by the crosslink density of the epoxy matrix, with higher toughenability for lower crosslink density epoxies. Key operative toughening mechanisms of the above model BCP-toughened epoxies were found to be nanoparticle cavitation-induced matrix shear banding for the low crosslink density epoxies. The toughening effect from BCP nanoparticles was also compared with core-shell rubber-toughened epoxies having different levels of crosslink density. The usefulness of the present findings for designing toughened thermosetting materials with desirable properties is discussed.     

Poly(dibenzodiazocine)s: analysis of low molecular weight fractions by MALDI-TOF MS

Poly(dibenzodiazocine)s, members of a new class of polyimines with high thermal stability and solubility in organic solvents, were synthesized from 2-amino-4′-fluorobenzophenone and three bisphenols. The high molecular weight polymers were shown by MALDI-TOF mass spectra to be accompanied by low molecular weight linear oligomers with the expected end group combinations and low molecular weight cyclic oligomers. The yields of the smaller cyclics were raised using a pseudo-dilution polymerization method.     

Expression of nitric oxide synthase isoforms (NOS II and NOS III) in adult rat lung in hyperoxic pulmonary hypertension

Breathing air with a high oxygen tension induces an inflammatory response and injures the microvessels of the lung. The resulting development of smooth muscle cells in these segments contributes to changes in vasoreactivity and increased pulmonary artery pressure. This in vivo study determines the temporal and spatial expression of endogenous endothelial nitric oxide synthase (NOS III) and inducible NOS (NOS II), important enzymes regulating vasoreactivity and inflammation, in the adult rat lung during the development of experimental pulmonary hypertension induced by oxidant injury. We analyzed the cellular distribution of these NOS isoforms, using specific antibodies, and assessed enzyme activity at baseline and after 1-28 days of hyperoxia (FIO2 0.87). The number of NOS III-immuno-positive endothelial cells increased early in hyperoxia and then remained high. By day 28, the relative number of these cells had increased from 40% in proximal vessels and 13-16% in distal alveolar vessels of the normal lung to 73-86% and 40-59%, respectively, in hyperoxia. Pulmonary alveolar macrophages (PAMs), normally few in number and only weakly immunopositive for NOS II or III in the normal lung, increased in number in hyperoxia and were strongly immunopositive for each isoform. These morphological data were supported by a temporal increase in total and calcium-independent NOS activity. Thus NOS expression and activity significantly increased in hyperoxia as pulmonary hypertension developed, and NOS III expression increased selectively in vascular endothelial cells, while both NOS isoforms were expressed by the PAM population. We conclude that this increase in expression of a potent vasodilator, an antiproliferative agent for smooth muscle cells, and an antioxidant molecule represents an adaptive response to protect the lung from oxidant-induced vascular and epithelial injury.