Induction of tumor-specific T-cell responses by vaccination with tumor lysate-loaded dendritic cells in colorectal cancer patients with carcinoembryonic-antigen positive tumors

Background Dendritic cells (DCs) are the most effective antigen-presenting cells. In the last decade, the use of DCs for immunotherapy of cancer patients has been vastly increased. High endocytic capacity together with a unique capability of initiating primary T-cell responses have made DCs the most potent candidates for this purpose. Although DC vaccination occasionally leads to tumor regression, clinical efficacy, and immunogenicity of DCs in clinical trials has not been yet clarified. The present study evaluated the safety and effectiveness of tumor-lysate loaded DC vaccines in advanced colorectal cancer (CRC) patients with carcinoembryonic antigen (CEA) positive tumors. Results Six patients HLA-A*0201-positive were vaccinated with autologous DCs loaded with tumor lysates (TL) together with tetanus toxoid antigen, hepatitis B, and influenza matrix peptides. Two additional patients were injected with DCs that were generated from their sibling or parent with one haplotype mismatch. All patients received the vaccines every 2 weeks, with a total of three intra-nodal injections per patient. The results indicated that DC vaccination was safe and well tolerated by the patients. Specific immune responses were detected and in some patients, transient stabilization or even reduction of CEA levels were observed. The injection of haplotype mismatched HLA-A*0201-positive DCs resulted in some enhancement of the anti-tumor response in vitro and led to stabilization/reduction of CEA levels in the serum, compared to the use of autologous DCs. Conclusion Altogether, these results suggest that TL-pulsed DCs may be an effective vaccine method in CRC patients. Elimination of regulatory mechanisms as well as adjustment of the vaccination protocol may improve the efficacy of DC vaccination. An erratum to this article can be found at     

Epiphytic lichen is associated with species richness of gall-inducing aphids but not with niche differentiation among them

The presence of epiphytic foliose lichen amplifies the heterogeneity of habitat by creating shelters for insects living on tree bark. It thus should enhance species number and spatial niche segregation among these canopy insects. We studied this hypothesis in a field experiment using four aphid species that induce galls on Pistacia atlantica trees covered with Xanthoria parietina lichen. In autumn 2008, 3 months after aphid fundatrices were oviposited, we marked six branches on each of 29 trees. Two served as a control, whereas the other four were isolated with insect glue; two of them were scraped with sandpaper to remove epiphytic foliose lichens. We therefore obtained three treatments comprising control branches, isolated branches with lichen, and isolated branches without lichen. In summer 2009, we counted all the galls developing on five new annual shoots on each of 174 branches. We observed more cecidogenic aphid species on all the branches with lichens than without, but each species at different proportions. The different frequencies of utilization of the lichen did not lead to habitat partitioning between species. In conclusion, although habitat heterogeneity itself was associated with species richness and population abundance, it did not induce spatial niche segregation. Considering that many economically important insect species, pests and natural enemies, oviposit or spend some portion of their lives in bark cracks, it is possible that some can use lichens too for protection or/and oviposition sites. As a consequence, lichens may affect management of agrosystems and their impacts should be investigated more deeply in such contexts.     

The nuts and bolts of germ-cell migration

In many species, primordial germ cells (PGCs) migrate from the position where they are specified to the site where the gonad develops, where they differentiate into sperm and egg. Germ cells thus serve as an excellent model for studying cell migration in the context of the live organism. In recent years, a number of cues directing the migration of the cells towards their target were identified and some of the relevant molecules and biochemical pathways were revealed. In this review we present those results, focusing on 'cell mechanics' of the process including cell adhesion, traction generation and cell polarization.     

Discovering local patterns of co - evolution: computational aspects and biological examples

Background

Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local.

Results

In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution, signaling pathways that are related to neurotransmission exhibit a relatively higher level of co-evolution along the primate subtree.

Conclusions

We show that finding local patterns of co-evolution is a computationally challenging task and we offer novel algorithms that allow us to solve this problem, thus opening a new approach for analyzing the evolution of biological systems.     

Matrix metalloproteinase-7 activation of mouse paneth cell pro-alpha-defensins: SER43 down arrow ILE44 proteolysis enables membrane-disruptive activity

Small intestinal Paneth cells secrete alpha-defensin microbicidal peptides as mediators of innate enteric immunity. In mice, production of mature Paneth cell alpha-defensins, termed cryptdins (Crps), requires proteolytic activation of inactive precursors (pro-Crps) by the convertase matrix metalloproteinase-7. Proteolysis of mouse (pro-Crp4)(20-92) produces the specific cleavage intermediates pro-Crp4(44-92), pro-Crp4(54-92), and pro-Crp4(59-92). To identify which cleavage event enables bactericidal activity, recombinant pro-Crp4-processing intermediates were purified to homogeneity and assayed for bactericidal peptide activity. The in vitro bactericidal activities of pro-Crp4-processing intermediates were very similar to fully processed Crp4, contrasting the lack of bactericidal and membrane-disruptive activity shown by pro-Crp4(20-92). Thus, cleavage of pro-Crp4(20-92) at Ser(43) downward arrowIle(44) is sufficient to activate bactericidal activity, and amino acids in the pro-Crp4(20-43) of the proregion maintain the precursor in an inactive state. Because cationic Arg residues are determinants of Crp4 bactericidal peptide activity, we hypothesized that Asp and Glu residues in pro-Crp4(20-43) neutralize Crp4 Arg side chains in pro-Crp4(20-92). Therefore, a pro-Crp4(20-92) variant with Gly substitutions at all pro-Crp4(20-43) Asp and Glu positions ((DE/G)-pro-Crp4) was prepared, and it was bactericidal and lysed phospholipid vesicles under conditions where native pro-Crp4(20-92) lacks activity. These findings show that MMP-7 proteolysis of pro-Crp4(20-92) at Ser(43) downward arrowIle(44) converts inactive precursors to bactericidal forms by removal of covalently associated, inhibitory acidic amino acids from proximity with the Crp4 component of the molecule.     

Typologies of attentional networks

Attention is a central theme in cognitive science - it exemplifies the links between the brain and behaviour, and binds psychology to the techniques of neuroscience. A visionary model suggested by Michael Posner described attention as a set of independent control networks. This challenged the previously held view of attention as a uniform concept. The idea that disparate attentional networks correlate with discrete neural circuitry and can be influenced by focal brain injuries, mental state and specific drugs has since been supported by converging data from several modern methodologies. Given the recent explosion in empirical data, attentional typologies provide powerful conceptual tools with which to contextualize and integrate these findings.     

Characterization of Escherichia coli null mutants for glutaredoxin 2.

Three Escherichia coli glutaredoxins catalyze GSH-disulfide oxidoreductions, but the atypical 24-kDa glutaredoxin 2 (Grx2, grxB gene), in contrast to the 9-kDa glutaredoxin 1 (Grx1, grxA gene) and glutaredoxin 3 (Grx3, grxC gene), is not a hydrogen donor for ribonucleotide reductase. To improve the understanding of glutaredoxin function, a null mutant for grxB (grxB(-)) was constructed and combined with other mutations. Null mutants for grxB or all three glutaredoxin genes were viable in rich and minimal media with little changes in their growth properties. Expression of leaderless alkaline phosphatase showed that Grx1 and Grx2 (but not Grx3) contributed in the reduction of cytosolic protein disulfides. Moreover, Grx1 could catalyze disulfide formation in the oxidizing cytosol of combined null mutants for glutathione reductase and thioredoxin 1. grxB(-) cells were more sensitive to hydrogen peroxide and other oxidants and showed increased carbonylation of intracellular proteins, particularly in the stationary phase. Significant up-regulation of catalase activity was observed in null mutants for thioredoxin 1 and the three glutaredoxins, whereas up-regulation of glutaredoxin activity was observed in catalase-deficient strains with additional defects in the thioredoxin pathway. The expression of catalases is thus interconnected with the thioredoxin/glutaredoxin pathways in the antioxidant response.