Immunodominant Francisella tularensis antigens identified using proteome microarray

Stimulation of protective immune responses against intracellular pathogens is difficult to achieve using non-replicating vaccines. BALB/c mice immunized by intramuscular injection with killed Francisella tularensis (live vaccine strain) adjuvanted with preformed immune stimulating complexes admixed with CpG, were protected when systemically challenged with a highly virulent strain of F. tularensis (Schu S4). Serum from immunized mice was used to probe a whole proteome microarray in order to identify immunodominant antigens. Eleven out of the top 12 immunodominant antigens have been previously described as immunoreactive in F. tularensis. However, 31 previously unreported immunoreactive antigens were revealed using this approach. Twenty four (50%) of the ORFs on the immunodominant hit list belonged to the category of surface or membrane associated proteins compared to only 22% of the entire proteome. There were eight hypothetical protein hits and eight hits from proteins associated with different aspects of metabolism. The chip also allowed us to readily determine the IgG subclass bias, towards individual or multiple antigens, in protected and unprotected animals. These data give insight into the protective immune response and have potentially important implications for the rational design of non-living vaccines for tularemia and other intracellular pathogens.     

A Monte Carlo evaluation for effects of probable dimensional uncertainties of low dose rate brachytherapy seeds on dose

The aim of this study is to determine effects of size deviations of brachytherapy seeds on two dimensional dose distributions around the seed. Although many uncertainties are well known, the uncertainties which stem from geometric features of radiation sources are weakly considered and predicted. Neither TG-43 report which is not completely in common consensus, nor individual scientific MC and experimental studies include sufficient data for geometric uncertainties. Sizes of seed and its components can vary in a manufacturing deviation. This causes geometrical uncertainties, too. In this study, three seeds which have different geometrical properties were modeled using EGSnrc-Code Packages. Seeds were designed with all their details using the geometry package. 5% deviations of seed sizes were assumed. Modified seeds were derived from original seed by changing sizes by 5%. Normalizations of doses which were calculated from three kinds of brachytherapy seed and their derivations were found to be about 3%–20%. It was shown that manufacturing differences of brachytherapy seed cause considerable changes in dose distribution.     

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques

MOTIVATION: We present a study of antigen expression signals from a newly developed high-throughput protein microarray technique. These signals are a measure of antibody-antigen binding activity and provide a basis for understanding humoral immune responses to various infectious agents and supporting vaccine and diagnostic development. RESULTS: We investigate the characteristics of these expression profiles and show that noise models, normalization, variance estimation and differential expression analysis techniques developed in the context of DNA microarray analysis can be adapted and applied to these protein arrays. Using a high-dimensional dataset containing measurements of expression profiles of antibody reactivity against each protein (295 antigens and 9 controls) in 42 malaria (Plasmodium falciparum) protein arrays derived from 22 donors with various clinical presentations of malaria, we present a methodology for the analysis and identification of significantly expressed antigens targeted by immune responses for individual sera, groups of sera and across stages of infection. We also conduct a short study highlighting the top immunoreactive antigens where we identify three novel high priority antigens for future evaluation. AVAILABILITY: All software programs (in R) used for the analysis described in this paper are freely available for academic purposes at www.igb.uci.edu/servers/servers.html.     

Forest stand structure, composition, and dynamics in 34 sites over Japan

This data paper reports tree census data collected in a network of 34 forest sites in Japan. This is the largest forest data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Forty-two permanent plots, usually 1?ha in size, were established in old-growth or secondary natural forests. Censuses of woody species ??15?cm girth at breast height were conducted every year or once during 2004 to 2009. The data provide species abundance, survivorship and stem girth growth of 52,534 individuals of 334 tree and liana species. The censuses adopted common census protocol, which provide good opportunities for meta-analyses and comparative studies among forests. The data have been used for ecological studies as well as for the biodiversity reports published by the Ministry of the Environment.     

Evaluation of two different adjuvants with immunogenic uroplakin 3A-derived peptide for their ability to evoke an immune response in mice

Rationale

Organ- or tissue-specific antigens produced by normal tissue or by cancer cells could be used in cancer immunotherapy, to target the tumor. In our previous study, we induced T-cell-mediated, bladderspecific autoimmunity by targeting the bladder-specific protein Uroplakin 3A (UPK3A). UPK3A is a well-chosen target for developing an autoimmune response against bladder cancer since the antigen is also expressed in bladder tumors. To use this peptide, which was derived from the UPK3A protein in a bladder cancer vaccine study, it is necessary to induce a strong immune response. In this study, we aimed to develop a robust immune response in BALB/c mice using the well-characterized keyhole limpet hemocyanin (KLH)-conjugated peptide antigen (UPK3A 65-84) conjugated with an immunogenic carrier protein. In combination with the peptide, we used either Freund’s complete adjuvant (CFA) or CpG (cytosine-phosphate-guanine oligonucleotides) as effective adjuvants in order to overcome tumor tolerance.

Objectives

The immune response evoked by UPK3A 65-84 peptide, using two different adjuvants, was compared by detection of changes in the proliferative response of immune cells, in the cytokine profile, and in the immune cell populations.

Findings

We demonstrated that CpG, combined with KLH-UPK3A 65-84, promoted a more robust immune response, via induction of higher IL-2, IFN-γ, TNF-α, IL-17 production and activation of more immune cells (CD4⁺ T cells, CD8⁺ T cells, NK cells CD11b, CD45), than CFA and the KLHUPK3A 65-84.

Conclusion

CpG as an adjuvant combined with KLH-UPK3A 65-84 could be used in preclinical models of bladder cancer for the development of cancer immunotherapy strategies.

     

Cholesterol-related gene variants are associated with diabetes in coronary artery disease patients

Molecular Biology Reports - Coronary artery disease (CAD) which is a complex cardiovascular disease is the leading cause of death worldwide. The changing prevalence of the disease in different...     

In vitro and in silico studies of nitrobenzamide derivatives as potential anti-neuroinflammatory agents

Communicated by Ramaswamy H. Sarma