Targeting the gut vascular endothelium induces gut effector CD8 T cell responses via cross-presentation by dendritic cells

Systemic delivery of Ag usually induces poor mucosal immunity. To improve the CD8 T cell response at mucosal sites, we targeted the Ag to MAdCAM-1, a mucosal addressin cell adhesion molecule expressed mainly by high endothelial venules (HEV) in mesenteric lymph nodes (MLN) and Peyer's patches of gut-associated lymphoid tissue. When chemical conjugates of anti-MAdCAM-1 Ab and model Ag OVA were injected i.v., a greatly enhanced proliferative response of Ag-specific OT-I CD8 T cells was detected in MLN. This was preceded by prolonged accumulation, up to 2 wk, of the anti-MAdCAM OVA conjugate on HEV of Peyer's patches and MLN. In contrast, nontargeted OVA conjugate was very inefficient in inducing OT-I CD8 T cell proliferation in MLN and required at least 20-fold more Ag to induce a comparable response. In addition, MAdCAM targeting elicits an endogenous OVA-specific CD8 T cell response, evident by IFN-gamma production and target killing. Induced response offers protection against an OVA-expressing B cell lymphoma. We propose that the augmentation of gut CD8 T cell responses by MAdCAM targeting is due to both accumulation of Ag in the HEV and conversion of a soluble Ag to a cell-associated one, allowing cross-presentation by DCs.     

N-glycolyl GM1 ganglioside as a receptor for simian virus 40

Carbohydrate microarrays have emerged as powerful tools in analyses of microbe-host interactions. Using a microarray with 190 sequence-defined oligosaccharides in the form of natural glycolipids and neoglycolipids representative of diverse mammalian glycans, we examined interactions of simian virus 40 (SV40) with potential carbohydrate receptors. While the results confirmed the high specificity of SV40 for the ganglioside GM1, they also revealed that N-glycolyl GM1 ganglioside [GM1(Gc)], which is characteristic of simian species and many other nonhuman mammals, is a better ligand than the N-acetyl analog [GM1(Ac)] found in mammals, including humans. After supplementing glycolipid-deficient GM95 cells with GM1(Ac) and GM1(Gc) gangliosides and the corresponding neoglycolipids with phosphatidylethanolamine lipid groups, it was found that GM1(Gc) analogs conferred better virus binding and infectivity. Moreover, we visualized the interaction of NeuGc with VP1 protein of SV40 by molecular modeling and identified a conformation for GM1(Gc) ganglioside in complex with the virus VP1 pentamer that is compatible with its presentation as a membrane receptor. Our results open the way not only to detailed studies of SV40 infection in relation to receptor expression in host cells but also to the monitoring of changes that may occur with time in receptor usage by the virus.     

Modeling cancer: integration of "omics" information in dynamic systems

The last 10 years have seen the rise of many technologies that produce an unprecedented amount of genome-scale data from many organisms. Although the research community has been successful in exploring these data, many challenges still persist. One of them is the effective integration of such data sets directly into approaches based on mathematical modeling of biological systems. Applications in cancer are a good example. The bridge between information and modeling in cancer can be achieved by two major types of complementary strategies. First, there is a bottom-up approach, in which data generates information about structure and relationship between components of a given system. In addition, there is a top-down approach, where cybernetic and systems-theoretical knowledge are used to create models that describe mechanisms and dynamics of the system. These approaches can also be linked to yield multi-scale models combining detailed mechanism and wide biological scope. Here we give an overall picture of this field and discuss possible strategies to approach the major challenges ahead.     

Helix-loop-helix protein p8, a transcriptional regulator required for cardiomyocyte hypertrophy and cardiac fibroblast matrix metalloprotease induction

Cardiomyocyte hypertrophy and extracellular matrix remodeling, primarily mediated by inflammatory cytokine-stimulated cardiac fibroblasts, are critical cellular events in cardiac pathology. The molecular components governing these processes remain nebulous, and few genes have been linked to both hypertrophy and matrix remodeling. Here we show that p8, a small stress-inducible basic helix-loop-helix protein, is required for endothelin- and alpha-adrenergic agonist-induced cardiomyocyte hypertrophy and for tumor necrosis factor-stimulated induction, in cardiac fibroblasts, of matrix metalloproteases (MMPs) 9 and 13-MMPs linked to general inflammation and to adverse ventricular remodeling in heart failure. In a stimulus-dependent manner, p8 associates with chromatin containing c-Jun and with the cardiomyocyte atrial natriuretic factor (anf) promoter and the cardiac fibroblast mmp9 and mmp13 promoters, established activator protein 1 effectors. p8 is also induced strongly in the failing human heart by a process reversed upon therapeutic intervention. Our results identify an unexpectedly broad involvement for p8 in key cellular events linked to cardiomyocyte hypertrophy and cardiac fibroblast MMP production, both of which occur in heart failure.     

A systems biology analysis of protein-protein interactions between yeast superoxide dismutases and DNA repair pathways

Superoxide dismutases (SODs) are widely distributed in eukaryotic and prokaryotic species and are responsible for O(2)(.-) scavenging and dismutation to H(2)O(2) and O(2). Mutations in the cytoplasmic (Sod1p) or mitochondrial (Sod2p) form of SODs result in aging, neurodegenerative diseases, and carcinogenesis. Diminished activity of SODs leads to reduced activity of DNA repair pathways, and overexpression of SODs in cells defective for DNA repair increases their level of chromatin damage. Unfortunately, little is understood regarding the interplay between SODs and DNA repair proteins and their role in protecting the genome from oxidative damage. To elucidate the association between yeast SODs and DNA repair mechanisms, a systems biology study was performed employing algorithms of literature data mining and the construction of physical protein-protein interactions from large yeast protein databases. The results obtained in this work allow us to draw two models suggesting that yeast SODs act as O(2)(.-) sensors under conditions of redox imbalance, activating and controlling specific DNA repair mechanisms (e.g., recombinational and excision repair pathways), chromatin remodeling, and synthesis of dNTPs.     

Horseradish peroxidase in ionic liquids: Reactions with water insoluble phenolic substrates

The reactivity of horseradish peroxidase (HRP) with water insoluble phenolic compounds has been studied in 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF₄])/water mixtures. The enzyme retained some catalytic activity up to 90% ionic liquid in water at 25 °C only at pH values higher than 9.0. Activity steadily decreased towards neutral and acidic conditions, as judged by 4-aminoantypirin/phenol activity tests. Inhibition of horseradish peroxidase under neutral acidic condition was due to the binding of fluoride anions released from tetrafluoroborate anion to the heme iron as demonstrated by the sharp UV–visible absorption transition diagnostic of the conversion from a five coordinated to a six coordinated high spin ferric heme iron. Thus, reactions with water insoluble phenols were carried out under alkaline reaction conditions and 75% [BMIM][BF₄]/water mixture. Under these conditions, the distribution of the reaction products was much narrower with respect to that observed in aqueous buffers or water/dimethylformamide or water/dimethylsulfoxide mixtures, and polymeric species other than dimers were not observed. Technical scale preparations of a novel 4-phenylphenol ortho dimer [2,2′-bi-(4-phenylphenol)] with a high yield of the desired product were obtained.     

Anti-Sporothrix Antibody Detection in Domestic Cats as an Indicator of a Possible New Occurrence Area for Sporotrichosis in North Brazil

Mycopathologia - Feline sporotrichosis has emerged as an important public health issue in some countries, especially Brazil. Currently, zoonotic transmission of Sporothrix brasiliensis by domestic...     

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq).We applied ChIP-seq to map the chromosomal binding sites for two ISWI-containing nucleosome remodeling factors, ACF and RSF, in Drosophila embryos. Employing several polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF-1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters.Further validation included controls using chromatin of mutant embryos that do not express ACF1 or RSF-1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and appear as ‘Phantom Peaks’. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin.Mining the modENCODE ChIP-seq profiles identifies potential Phantom Peaks in many profiles of epigenetic regulators. These profiles and other ChIP-seq data featuring prominent Phantom Peaks must be validated with chromatin from cells in which the protein of interest has been depleted.