KnotProt: a database of proteins with knots and slipknots.

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints

Dopant clustering and vacancy ordering in neodymium doped ceria

Lanthanide doped cerias, show fast oxide ion conduction and have applications as electrolytes in intermediate temperature solid oxide fuel cells. Here, we examine the long- and short-range structures of Ce1−xNdxO2−x/2 (0.05 ≤ x ≤ 0.30, NDC) using reverse Monte Carlo modelling of total neutron scattering data, supported by measurements of electrical behaviour using a.c. impedance spectroscopy. Three distinct features are evident in the local structure of NDC, viz.: clustering of Nd3+ cations, preferred Nd3+-oxide ion vacancy association and oxide ion vacancy clustering with preferential alignment in the 〈100〉 direction. Interestingly, the presence of preferential dopant cation-oxide ion vacancy association is also observed at 600 °C, although diminished compared to the level at room temperature. This suggests a continued contribution of defect association enthalpy to activation energy at elevated temperatures and is reflected in similar compositional variation of high- and low-temperature activation energies

Deuteron-deuteron collision at 160 MeV

The experiment was carried out using BINA detector at KVI in Groningen. For the first time an extensive data analysis of the data collected in back part of the detector is presented, where a clusterization method is utilized for angular and energy information. We also present differential cross-sections for the (dd$\rightarrow$dpn) breakup reaction within \textit{dp} quasi-free scattering limit and their comparison with first calculations based on Single Scattering Approximation (SSA) approach.Comment: 6 pages, 4 figures, presented at Jagiellonian Symposium 2015 in Krakow, PhD wor

Effects of dietary plant-derived phytonutrients on the genome-wide profiles and coccidiosis resistance in the broiler chickens

<p>Abstract</p> <p>Background</p> <p>The present study was conducted to investigate the effects of dietary plant-derived phytonutrients, carvacrol, cinnamaldehyde and Capsicum oleoresin, on the translational regulation of genes associated with immunology, physiology and metabolism using high-throughput microarray analysis and <it>in vivo</it> disease challenge model of avian coccidiosis.</p> <p>Methods</p> <p>In this study, we used nutrigenomics technology to investigate the molecular and genetic mechanisms of dietary modulation of host innate immunity and metabolism by three phytonutrients. To validate their immunomodulatory effects in a disease model, young broiler chickens fed a standard diet supplemented with three phytochemicals (carvacrol, cinnamaldehyde, and Capsicum oleoresin) from one day post-hatch were orally challenged with <it>E. acervulina</it>. The body weight gain and fecal oocyst production were used to evaluate coccidiosis disease parameters.</p> <p>Results</p> <p>Analysis of global gene expression profiles of intestinal tissues from phytonutrient-fed birds indicated that Capsicum oleoresin induced the most gene changes compared to the control group where many of these genes were associated with those of metabolism and immunity. The most reliable network induced by dietary cinnamaldehyde treatment was related with the functions of antigen presentation, humoral immune response, and inflammatory disease. Furthermore, dietary supplementation with these phytonutrients significantly protected broiler chickens against live coccidiosis challenge infection based on body weight and parasite fecundity.</p> <p>Conclusions</p> <p>The results of this study provide clear evidence to support the idea that plant-derived phytochemicals possess immune-enhancing properties in chickens and these new findings create a new possibility to develop effective drug-free alternative strategies for disease control for poultry infectious diseases.</p