MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors

T cell receptor (TCR) recognition of peptide-MHC class I (pMHC) complexes is a crucial event in the adaptive immune response to pathogens. Peptide epitopes often display a strong dominance hierarchy, resulting in focusing of the response on a limited number of the most dominant epitopes. Such T cell responses may be additionally restricted by particular MHC alleles in preference to others. We have studied this poorly understood phenomenon using Theileria parva, a protozoan parasite that causes an often fatal lymphoproliferative disease in cattle. Despite its antigenic complexity, CD8+ T cell responses induced by infection with the parasite show profound immunodominance, as exemplified by the Tp1(214-224) epitope presented by the common and functionally important MHC class I allele N*01301. We present a high-resolution crystal structure of this pMHC complex, demonstrating that the peptide is presented in a distinctive raised conformation. Functional studies using CD8+ T cell clones show that this impacts significantly on TCR recognition. The unconventional structure is generated by a hydrophobic ridge within the MHC peptide binding groove, found in a set of cattle MHC alleles. Extremely rare in all other species, this feature is seen in a small group of mouse MHC class I molecules. The data generated in this analysis contribute to our understanding of the structural basis for T cell-dependent immune responses, providing insight into what determines a highly immunogenic p-MHC complex, and hence can be of value in prediction of antigenic epitopes and vaccine design.

A predictor of membrane class:discriminating α-helical and β-barrel membrane proteins from non-membranous proteins

Accurate protein structure prediction remains an active objective of research in bioinformatics. Membrane proteins comprise approximately 20% of most genomes. They are, however, poorly tractable targets of experimental structure determination. Their analysis using bioinformatics thus makes an important contribution to their on-going study. Using a method based on Bayesian Networks, which provides a flexible and powerful framework for statistical inference, we have addressed the alignment-free discrimination of membrane from non-membrane proteins. The method successfully identifies prokaryotic and eukaryotic α-helical membrane proteins at 94.4% accuracy, β-barrel proteins at 72.4% accuracy, and distinguishes assorted non-membranous proteins with 85.9% accuracy. The method here is an important potential advance in the computational analysis of membrane protein structure. It represents a useful tool for the characterisation of membrane proteins with a wide variety of potential applications.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

On Minimizing ||S−(AX−XB)||Pp

In this paper, we minimize the map Fp (X)= ||S−(AX−XB)||Pp , where the pair (A, B) has the property (F P )Cp , S ∈ Cp , X varies such that AX − XB ∈ Cp and Cp denotes the von Neumann-Schatten class.

A Recession Notion for a Class of Monotone Bivariate Functions

Using monotone bifunctions, we introduce a recession concept for general equilibrium problems relying on a variational convergence notion. The interesting purpose is to extend some results of P. L. Lions on variational problems. In the process we generalize some results by H. Brezis and H. Attouch relative to the convergence of the resolvents associated with maximal monotone operators.

On a Class of Vertex Folkman Numbers

Let a1 , . . . , ar, be positive integers, i=1 ... r, m = ∑(ai − 1) + 1 and p = max{a1 , . . . , ar }. For a graph G the symbol G → (a1 , . . . , ar ) means that in every r-coloring of the vertices of G there exists a monochromatic ai -clique of color i for some i ∈ {1, . . . , r}. In this paper we consider the vertex Folkman numbers F (a1 , . . . , ar ; m − 1) = min |V (G)| : G → (a1 , . . . , ar ) and Km−1 ⊂ G} We prove that F (a1 , . . . , ar ; m − 1) = m + 6, if p = 3 and m ≧ 6 (Theorem 3) and F (a1 , . . . , ar ; m − 1) = m + 7, if p = 4 and m ≧ 6 (Theorem 4).

P-Sequential Spaces and Cleavability

∗ Supported by the Serbian Scientific Foundation, grant No 04M01

Applications of the Owa-Srivastava Operator to the Class of K-Uniformly Convex Functions

2000 Mathematics Subject Classification: Primary 30C45, 26A33; Secondary 33C15

On a Class of Fractional Type Integral Equations in Variable Exponent Spaces

2000 Mathematics Subject Classification: 45A05, 45B05, 45E05,45P05, 46E30

Problems for P-Monge-Ampere Equations

2010 Mathematics Subject Classification: 35A23, 35B51, 35J96, 35P30, 47J20, 52A40.

Characterization of the poxAB Operon Encoding a Class D Carbapenemase in Pseudomonas aeruginosa,

Pseudomonas aeruginosa is a dreaded opportunistic pathogen that causes severe and often intractable infections in immunocompromised and critically ill patients. This bacterium is also the primary cause of fatal lung infections in patients with cystic fibrosis and a leading nosocomial pathogen responsible for nearly 10% of all hospital-acquired infections. P. aeruginosa is intrinsically recalcitrant to most classes of antibiotics and has the ability to acquire additional resistance during treatment. In particular, resistance to the widely used β-lactam antibiotics is frequently mediated by the expression of AmpC, a chromosomally encoded β-lactamase that is ubiquitously found in P. aeruginosa strains. This dissertation delved into the role of a recently reported chromosomal β-lactamase in P. aeruginosa called PoxB. To date, no detailed studies have addressed the regulation of poxB expression and its contribution to β-lactam resistance in P. aeruginosa. In an effort to better understand the role of this β-lactamase, poxB was deleted from the chromosome and expressed in trans from an IPTG-inducible promoter. The loss of poxB did not affect susceptibility. However, expression in trans in the absence of ampC rendered strains more resistant to the carbapenem β-lactams. The carbapenem-hydrolyzing phenotype was enhanced, reaching intermediate and resistant clinical breakpoints, in the absence of the carbapenem-specific outer membrane porin OprD. As observed for most class D β-lactamases, PoxB was only weakly inhibited by the currently available β-lactamase inhibitors. Moreover, poxB was shown to form an operon with the upstream located poxA, whose expression in trans decreased pox promoter (Ppox) activity suggesting autoregulation. The transcriptional regulator AmpR negatively controlled Ppox activity, however no direct interaction could be demonstrated. A mariner transposon library identified genes involved in the transport of polyamines as potential regulators of pox expression. Unexpectedly, polyamines themselves were able induce resistance to carbapenems. In summary, P. aeruginosa carries a chromosomal-encoded β-lactamase PoxB that can provide resistance against the clinically relevant carbapenems despite its narrow spectrum of hydrolysis and whose activity in vivo may be regulated by polyamines.

Does a mandibular RDP and new maxillary CD improve masticatory efficiency and quality of life in patients with a mandibular Kennedy class I arch?

Objectives To evaluate the change in masticatory efficiency and quality of life of patients treated with mandibular Kennedy class I removable partial dentures (RPDs) and maxillary complete dentures at the Department of Dentistry of the Federal University of Rio Grande do Norte. Materials and methods A total of 33 Kennedy class I patients were rehabilitated with maxillary complete dentures, and mandibular RPDs were selected for this non-randomized prospective intervention study. The patients had a mean age of 59.1 years. Masticatory efficiency was evaluated by colorimetric assay using fuchsin capsules. The measurements were conducted at baseline and 2 and 6 months after prosthesis insertion. Quality of life was evaluated using the Oral Health Impact Profile (OHIP-14) at baseline and 6 months after denture insertion. The Kolmogorov-Smirnov normality test was applied. Masticatory efficiency was evaluated by repeated measures ANOVA. Oral health-related quality of life was compared using the paired t test. Results There was no statistically significant difference in masticatory efficiency after denture insertion (p = 0.101). Significant differences were found (p = 0.010) for oral health-related quality of life. A significant improvement in psychological discomfort (p < 0.01) and psychological disability (p < 0.01) was observed. Mean difference value (95 % confidence interval) was 6.8 (3.8 to 9.7) points, reflecting a low impact of oral health on quality of life, considering the 0–56 range of variation of the OHIP-14 and a Cohen’s d of 1.13. Conclusion According to the results of the present study, rehabilitation with Kennedy class I RPDs and complete dentures did not influence masticatory efficiency but improved oral health-related quality of life. Clinical relevance The association between the patient’s quality of life and the masticatory efficiency is important for treatment predictability.