Defining the healthy "core microbiome" of oral microbial communities

Background  

Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).     

The Variable Hinge Region of Novel PKCs Determines Localization to Distinct Regions of the Immunological Synapse

The immunological synapse (IS) formed between a T cell and its cognate antigen-presenting cell (APC) enables the directional secretion of cytolytic and inflammatory molecules. Synaptic architecture is established in part by a two-step cascade of novel protein kinase C (nPKC) isozymes. PKCε and PKCη arrive at the IS first, and occupy the entire synaptic membrane. Then, PKCθ accumulates in a smaller zone at the center of the contact. We investigated the molecular basis for this differential recruitment behavior using chimeric nPKC constructs and total internal reflection fluorescence microscopy. Our studies revealed that the V3 linker just N-terminal to the kinase domain plays a crucial role in specifying nPKC localization. Substitution of this linker switched the scope and the kinetics of PKCθ accumulation to that of PKCε and PKCη, and vice versa. Although the V3 was necessary for synaptic compartmentalization, it was not sufficient, as the tandem C1 domains were also required to mediate membrane association. Together, these results suggest a model whereby the V3 linker controls nPKC sub-compartmentalization after initial C1 domain-mediated accumulation at the IS.     

Alternative 5’ Untranslated Regions Are Involved in Expression Regulation of Human Heme Oxygenase-1

The single nucleotide polymorphism rs2071746 and a (GT)_n microsatellite within the human gene encoding heme oxygenase-1 (HMOX1) are associated with incidence or outcome in a variety of diseases. Most of these associations involve either release of heme or oxidative stress. Both polymorphisms are localized in the promoter region, but previously reported correlations with heme oxygenase-1 expression remain not coherent. This ambiguity suggests a more complex organization of the 5’ gene region which we sought to investigate more fully.We evaluated the 5‘ end of HMOX1 and found a novel first exon 1a placing the two previously reported polymorphisms in intronic or exonic positions within the 5’ untranslated region respectively. Expression of exon 1a can be induced in HepG2 hepatoma cells by hemin and is a repressor of heme oxygenase-1 translation as shown by luciferase reporter assays. Moreover, minigene approaches revealed that the quantitative outcome of alternative splicing within the 5’ untranslated region is affected by the (GT)_n microsatellite.This data supporting an extended HMOX1 gene model and provide further insights into expression regulation of heme oxygenase-1. Alternative splicing within the HMOX1 5'' untranslated region contributes to translational regulation and is a mechanistic feature involved in the interplay between genetic variations, heme oxygenase-1 expression and disease outcome.     

Type II collagen-induced arthritis in mice. IV. Variations in immunogenetic regulation provide evidence for multiple arthritogenic epitopes on the collagen molecule

Type II collagen from six mammalian species was investigated for the capacity to induce an immune response and collagen-induced arthritis (CIA) in C57/B10 congenic mouse strains. H-2q haplotype mice were susceptible to chick, bovine, deer, rat, and human type II collagen, but were resistant to arthritis induced by porcine type II collagen. H-2r haplotype mice only developed CIA in response to bovine, deer, and porcine collagen. High antibody responses in the absence of disease, directed against a specific type II collagen, were observed in many independent haplotypes. The cross-reactive capacity of different antisera to the various collagen species was studied. The data support the existence of two arthritogenic and multiple nonarthritogenic epitopes on the type II collagen molecule.     

Gene transfer mediated by alpha2-macroglobulin.

alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in vitro. The alpha2-macroglobulin receptor is a very large and multifunctional cell surface receptor, whose rapid and efficient internalization rate makes it attractive for gene therapy, e.g. for hepatic gene targeting via injection into the portal vein.     

A physical model for motor proteins

A general stochastic theory is outlined for chemical to mechanical energy transduction by motor enzymes. In addition to ATP hydrolysis and fiber binding phenomena, thermal noise effects are taken into account. A minimal, 4-state model is identified that gives the hydrolysis rate as well as mechanical quantities such as sliding velocity and generated force, as functions of ATP concentration and the number of motors. It explains in a unified way many results of recent in vitro assays, both in myosins/actin and kinesins or dyneins/microtubule systems.     

Evidence for phosphorylation of yeast phosphofructokinase

Radioactively labelled material from yeast cells grown in the presence of [32P]phosphate was specifically recognized by antibodies raised against yeast phosphofructokinase. Purified yeast phosphofructokinase was phosphorylated in a cyclic AMP-independent manner by a protein kinase enriched from yeast extracts. This phosphorylation occurred specifically on the beta-subunit, and 0.56 mol of phosphate/mol of subunit was incorporated. The results indicate the phosphorylation of yeast phosphofructokinase both in vivo and in vitro. Phosphofructokinase phosphorylated in vitro was more stable against proteolytic degradation compared to the non-phosphorylated enzyme.     

Implementing behaviour in individual-based models using neural networks and genetic algorithms

Even though individual-based models (IBMs) have become very popular in ecology during the last decade, there have been few attempts to implement behavioural aspects in IBMs. This is partly due to lack of appropriate techniques. Behavioural and life history aspects can be implemented in IBMs through adaptive models based on genetic algorithms and neural networks (individual-based-neural network-genetic algorithm, ING). To investigate the precision of the adaptation process, we present three cases where solutions can be found by optimisation. These cases include a state-dependent patch selection problem, a simple game between predators and prey, and a more complex vertical migration scenario for a planktivorous fish. In all cases, the optimal solution is calculated and compared with the solution achieved using ING. The results show that the ING method finds optimal or close to optimal solutions for the problems presented. In addition it has a wider range of potential application areas than conventional techniques in behavioural modelling. Especially the method is well suited for complex problems where other methods fail to provide answers. This revised version was published online in July 2006 with corrections to the Cover Date.