SARS CTL Vaccine Candidates — HLA Supertype, Genome-Wide Scanning and Biochemical Validation

An effective SARS vaccine is likely to include components that can induce specific cytotoxic T-cell (CTL) responses. The specificities of such responses are governed by HLA-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information. The latter was recently established when a causative coronavirus (SARS CoV) was isolated and full-length sequenced. Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype, genome-wide scan for SARS-specific cytotoxic T cell epitopes. The scan includes all nine human HLA supertypes in total covering >99% of all major human populations. For each HLA supertype, we have selected the 15 top candidates for test in biochemical-binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.     

Temporomandibular joint: morphology and signal intensity characteristics of the disk at MR imaging

Magnetic resonance (MR) imaging has been used in the temporomandibular joint (TMJ) primarily to define the disk position. This report examines altered morphology and signal intensity characteristics of the TMJ disk as they relate to the severity of internal derangement. Two hundred sixteen joints in 133 patients with a history of such derangement. were imaged with MR. Disk position, signal intensity, morphology, and the presence of osteoarthritis were determined for each joint. The normal disk was not anteriorly displaced and had a normal "bow-tie" shape. A grade 1 disk was anteriorly displaced and had a normal shape; a grade 2 disk was anteriorly displaced and had an abnormal shape. Forty (19%) joints were considered normal; none of these exhibited osteoarthritis. One hundred thirty-nine (64%) joints were grade 1; osteoarthritis was found in 17%. Thirty-seven (17%) were grade 2; osteoarthritis was found in 95%. All forty normal joints had high or intermediate signal intensity in the disk. Osteoarthritic joints had a higher percentage of disks with diminished intensity (P less than .0001). Severe or untreated osteoarthritis is known to be a complication of TMJ internal derangements; hence this grading system seems to correlate with the severity of internal derangement.     

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions

Reverse immunogenetic approaches attempt to optimize the selection of candidate epitopes, and thus minimize the experimental effort needed to identify new epitopes. When predicting cytotoxic T cell epitopes, the main focus has been on the highly specific MHC class I binding event. Methods have also been developed for predicting the antigen-processing steps preceding MHC class I binding, including proteasomal cleavage and transporter associated with antigen processing (TAP) transport efficiency. Here, we use a dataset obtained from the SYFPEITHI database to show that a method integrating predictions of MHC class I binding affinity, TAP transport efficiency, and C-terminal proteasomal cleavage outperforms any of the individual methods. Using an independent evaluation dataset of HIV epitopes from the Los Alamos database, the validity of the integrated method is confirmed. The performance of the integrated method is found to be significantly higher than that of the two publicly available prediction methods BIMAS and SYFPEITHI. To identify 85% of the epitopes in the HIV dataset, 9% and 10% of all possible nonamers in the HIV proteins must be tested when using the BIMAS and SYFPEITHI methods, respectively, for the selection of candidate epitopes. This number is reduced to 7% when using the integrated method. In practical terms, this means that the experimental effort needed to identify an epitope in a hypothetical protein with 85% probability is reduced by 20-30% when using the integrated method.The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php.     

Cardiorespiratory fitness and body mass index values in 9-year-old rural Norwegian children

Aim: To describe cardiorespiratory fitness and body mass index (BMI) values in a representative population of 9-year-old Norwegian children in two rural communities and compare present values with previous findings.
Methods: Two hundred and fifty-nine 9-year-old children were invited, and 256 participated in this study. Maximal oxygen uptake was directly measured during a continuous progressive treadmill protocol. Body mass and height were also measured.
Results: The mean ± SD relative maximal oxygen uptake was 52.8 ± 6.5 for boys and 46.9 ± 7.2 mL/kg/min for girls. Eight percent of the boys and 16.8% of the girls were classified as overweight, and 1.6% of the boys and 6.9% of the girls as obese. Mean age, body mass, height and Ponderal index were not significantly different between sexes. Girls had a higher BMI than boys (p = 0.05).
Conclusion: Compared to earlier Norwegian studies, children's BMI values seem to have increased substantially. This increase is most pronounced in girls. When assessing these differences using the PI, this increase is less marked. Comparing maximal oxygen uptake data with that in earlier Nordic studies, there is no evidence that fitness has declined among 9-year olds. However, the limitations of the few earlier studies make reliable comparisons difficult.     

Ca2+ response in neutrophils after exposure to bacterial N-formyl-methionyl-leucyl-phenylalanine: delayed response in ulcerative colitis

OBJECTIVE: In acute stages of ulcerative colitis (UC), neutrophils migrate from the circulation into inflamed colonic tissue, initiated by yet unknown stimuli. The bacterial peptide N-formyl-methionyl-leucyl-phenylalanine (FMLP) is a component of the surface membrane of colonic bacteria such as Escherichia coli and stimulates Ca2+ influx into neutrophils, reflecting the fact that ionized calcium is an important secondary messenger for several neutrophil functions, including locomotion, phagocytosis and free oxygen radical production. Recent studies have revealed that Ca2+ dependent ICAM-1/beta 2-integrin mediated neutrophil migration is impaired in UC patients. The aim of the present work was to study the influx of Ca2+ into peripheral blood neutrophils of UC patients after exposure to FMLP and after binding of either beta 2-integrins or intercellular adhesion molecule-1 (ICAM-1). METHODS: The relative intracellular Ca2+ levels ([Ca2+]i ) were measured spectrofluorometrically in neutrophils isolated from eight UC patients and eight controls. The cells were exposed to 1 nm FMLP, 5 pm free ICAM-1, or antibodies binding ICAM-1 or the beta 2-integrins CD11a, CD11b, CD11c and CD18. RESULTS: A pronounced increase in [Ca2+]i was observed by exposure of cells to FMLP, and neutrophils from UC patients showed a consistent and significant delayed response as compared to cells from control subjects (P < 0.01). Antibody mediated cross-linking of CD18 triggered a small but detectable increase in [Ca2+]i, which did not differ between patients and controls. CONCLUSION: A delayed response to bacterial peptides appears to be a phenotypic trait for neutrophils of UC patients. A connection between FMLP stimulated Ca2+ influx and CD11/CD18 upregulation is discussed.     

Decreased prostaglandin E turnover in infants with essential fatty acid deficiency

Sick low birth weight infants (LBWI) are prone to develop rapid onset of essential fatty acid (EFA) deficiency. EFAs serve as precursors for prostaglandins (PGs). We measured the excretion of the major urinary metabolite of prostaglandins E1 and E2, 7alpha-hydroxy-5,11-diketotetranorprostane-1,16-dionic acid (PGE-M), in three EFA-deficient and in nine thriving neonates. There was no significant difference in PGE-M excretion between the sexes among thriving infants nor did PGE-M excretion appear to be affected by postconceptual age. However, a significant difference between the PGE-M excretion in the group of infants with EFA deficiency before and after treatment is apparent (P less than 0.05). Significant differences in PGE-M excretion were also found between the control group and the EFA-deficient infants. The severity of the EFA deficiency correlates directly with the degree of PGs excretion. The biochemical evidences of EFA deficiency and the decreased levels of PGE-M excretion are rapidly corrected when patients resume a diet containing EFA.     

Prostatic cancer therapy: comparison of external-beam radiation and I- 125 seed implantation treatment of stages B and C neoplasms

Of 179 patients with stage B or C adenocarcinoma of the prostate, 106 underwent iodine-125 seed-implant therapy (I-125 SI) and 73 received external-beam radiation therapy (EB). A retrospective analysis determined disease-free survival rate, local tumor control, and complication rate for each treatment group. The 5-year disease-free survival rates for SI-treated patients were 75% for stage B and 30% for stage C groups. Corresponding rates for EB-treated patients were 75% and 40%, respectively. The rate of local tumor control for stage B patients was 85% for SI-treated and 88% for EB-treated patients. The corresponding rates for stage C tumors were 75% for SI-treated and 92% for EB-treated patients. The rate of long-term complications in each group was approximately 10%. For stage B cancer of the prostate, I-125 SI treatment is an acceptable alternative to EB therapy; our data are inconclusive regarding stage C treatment, but EB therapy is preferred.