A Missing Switch in Peptide Exchange for MHC Class II Molecules

Introduction: Antigen processing and loading of peptides onto MHC class II molecules is a multistep process that involves vesicular transport of the MHCII molecules along the secretory pathway, where they eventually merge with antigen-containing endocytic vesicles or phagosomes (1). It is within these late endosomal or lysosomal compartments that protein antigens become degraded by proteases, most prominently by cathepsins, and where catalyzed peptide exchange by HLA-DM fulfills its role in the efficient replacement of the invariant chain-derived peptide CLIP by high-affinity pathogen- or host cell-derived peptides. Protease action may be limited by protein antigen abundance and redox conditions, while HLA-DM is regulated at several stages, including by expression levels, pH, or the co-expression of the competitive inhibitor HLA-DO. HLA-DM activity leads to significant changes in the immunopeptidome of antigen-presenting cells, thereby tailoring T cell responses and often shifting antigenicity toward high-affinity immunodominant epitopes (2). Control of DM activity by DO has been described to be of prime importance in thymic epithelial cells, in a subset of dendritic cells, and in B cells when entering the germinal centers for affinity maturation and class switching (3, 4). In all of these cases, the switch from a broader, self-peptide (CLIP) dominated immunopeptidome to a more focused repertoire is necessitated by the requirement for more stringent antigen presentation, often preceding more intense T cell reactivity and proliferation. Here, we review data on this cellular switch in the functionality of antigen presentation and propose that it is promoted by an as yet poorly understood molecular switch. Acknowledging that general biophysical parameters such as pH and redox are important for antigen processing in general, an elusive DM-DO switch is postulated that would allow rapid and strong shifts in immunopeptidomes. We capitalize on theoretical considerations to back our opinion that a regulatable switch would have the advantage of allowing for a rapid and possibly signal-dependent change in the peptide selection process, as might be required in the context of rapidly changing immunological conditions

Effektivität der internationalen Umweltschutzabkommen zum Mineralöltransport auf See und daraus abgeleitete Vorschläge zur Politikrevision

Die Studie untersucht die Effektivität internationaler Abkommen und Regelungen zum Umweltschutz beim Seetransport von Mineralöl (Erdöl). Begleitumstände und internationale Rechtsgrundlagen für die Umweltpolitik in diesem Feld werden dargestellt, direkte und indirekte Folgen der Politikinstrumente diskutiert. Obwohl die erklärten Ziele – die Eliminierung des bewußten und die Minimierung des unfallbedingten Eintrags von Mineralöl in die Meere – nicht erreicht wurden, kann doch von einem umweltpolitischen Erfolg gesprochen werden. Derzeit stehen die mit Gefälligkeitsflaggen verbundenen Probleme und Beschränkun-gen der Befugnisse und Zuständigkeiten der International Maritime Organization (IMO) der Vereinten Nationen effektiveren Politikinstrumenten zum Meeresumweltschutz entgegen. Die Analyse schließt mit Vorschlägen zur Politikrevision. Vorgeschlagen wird die Stärkung umweltbewußter Küstenstaaten im politischen Regime durch Einschränkung des Einflusses der Gefälligkeitsflaggen-Staaten und der Umbau der IMO in eine UN- Sonderorganisation zum Meeresumweltschutz auf See und maritimer Angelegenheiten. Wir danken Frank Biermann für Verbesserungsvorschläge zum ersten Entwurf dieses Aufsatzes und Manfred Binder für die kritische Durchsicht

Three-Dimensional Gradients of Cytokine Signaling between T Cells

Immune responses are regulated by diffusible mediators, the cytokines, which act at sub-nanomolar concentrations. The spatial range of cytokine communication is a crucial, yet poorly understood, functional property. Both containment of cytokine action in narrow junctions between immune cells (immunological synapses) and global signaling throughout entire lymph nodes have been proposed, but the conditions under which they might occur are not clear. Here we analyze spatially three-dimensional reaction-diffusion models for the dynamics of cytokine signaling at two successive scales: in immunological synapses and in dense multicellular environments. For realistic parameter values, we observe local spatial gradients, with the cytokine concentration around secreting cells decaying sharply across only a few cell diameters. Focusing on the well-characterized T-cell cytokine interleukin-2, we show how cytokine secretion and competitive uptake determine this signaling range. Uptake is shaped locally by the geometry of the immunological synapse. However, even for narrow synapses, which favor intrasynaptic cytokine consumption, escape fluxes into the extrasynaptic space are expected to be substantial (≥20% of secretion). Hence paracrine signaling will generally extend beyond the synapse but can be limited to cellular microenvironments through uptake by target cells or strong competitors, such as regulatory T cells. By contrast, long-range cytokine signaling requires a high density of cytokine producers or weak consumption (e.g., by sparsely distributed target cells). Thus in a physiological setting, cytokine gradients between cells, and not bulk-phase concentrations, are crucial for cell-to-cell communication, emphasizing the need for spatially resolved data on cytokine signaling

NNLO Photon Production with Realistic Photon Isolation

Isolated photon production at hadron colliders proceeds via direct production and fragmentation processes. Theory predictions for the isolated photon and photon-plus-jet cross section often impose idealised photon isolation criteria, eliminating the fragmentation contribution and introducing a systematic uncertainty in the comparison to data. We present NNLO predictions for the photon-plus-jet cross section with the experimental isolation including both, direct and fragmentation contributions. Predictions with two different parton-to-photon fragmentation functions are compared, allowing for an estimation of the uncertainty stemming from the only loosely constrained photon fragmentation functions

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type-specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors depends on their genomic context. The mostly unmethylated CpG islands have reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides are preferentially associated with nucleosomes. In contrast, outside of CpG islands most CpGs are methylated, and the average methylation density oscillates so that it is highest in the linker region between nucleosomes. Outside CpG islands, binding of TET1, an enzyme that converts 5mC to 5hmC, is associated with labile, MNase-sensitive nucleosomes. Such nucleosomes are poised for eviction in ESCs and become stably bound in differentiated cells where the TET1 and 5hmC levels go down. This process regulates a class of CTCF binding sites outside CpG islands that are occupied by CTCF in ESCs but lose the protein during differentiation. We rationalize this cell type-dependent targeting of CTCF with a quantitative biophysical model of competitive binding with the histone octamer, depending on the TET1, 5hmC, and 5mC state

Ferropericlase inclusions in ultradeep diamonds from Sao Luiz (Brazil): High Li abundances and diverse Li-isotope and trace element compositions suggest an origin from a subduction mélange

The most remarkable feature of the inclusion suite in ultradeep alluvial and kimberlitic diamonds from Sao Luiz (Juina area in Brazil) is the enormous range in Mg# [100xMg/(Mg + Fe)] of the ferropericlases (fper). The Mg-richer ferropericlases are from the boundary to the lower mantle or from the lower mantle itself when they coexist with ringwoodite or Mg- perovskite (bridgmanite). This, however, is not an explanation for the more Fe-rich members and a lowermost mantle or a “D” layer origin has been proposed for them. Such a suggested ultra-deep origin separates the Fe-rich fper-bearing diamonds from the rest of the Sao Luiz ultradeep diamond inclusion suite, which also contains Ca-rich phases. These are now thought to have an origin in the uppermost lower mantle and in the transition zone and to belong either to a peridotitic or mafic (subducted oceanic crust) protolith lithology. We analysed a new set of more Fe-rich ferropericlase inclusions from 10 Sao Luiz ultradeep alluvial diamonds for their Li isotope composition by solution MC-ICP-MS (multi collector inductively coupled plasma mass spectrometry), their major and minor elements by EPMA (electron probe micro-analyser) and their Li-contents by SIMS (secondary ion mass spectrometry), with the aim to understand the origin of the ferropericlase protoliths. Our new data confirm the wide range of ferropericlase Mg# that were reported before and augment the known lack of correlation between major and minor elements. Four pooled ferropericlase inclusions from four diamonds provided sufficient material to determine for the first time their Li isotope composition, which ranges from δ7Li + 9.6 ‰ to −3.9 ‰. This wide Li isotopic range encompasses that of serpentinized ocean floor peridotites including rodingites and ophicarbonates, fresh and altered MORB (mid ocean ridge basalt), seafloor sediments and of eclogites. This large range in Li isotopic composition, up to 5 times higher than ‘primitive upper mantle’ Li-abundances, and an extremely large and incoherent range in Mg# and Cr, Ni, Mn, Na contents in the ferropericlase inclusions suggests that their protoliths were members of the above lithologies. This mélange of altered rocks originally contained a variety of carbonates (calcite, magnesite, dolomite, siderite) and brucite as the secondary products in veins and as patches and Ca-rich members like rodingites and ophicarbonates. Dehydration and redox reactions during or after deep subduction into the transition zone and the upper parts of the lower mantle led to the formation of diamond and ferropericlase inclusions with variable compositions and a predominance of the Ca-rich, high-pressure silicate inclusions. We suggest that the latter originated from peridotites, mafic rocks and sedimentary rocks as redox products between calcite and SiO2

DynPeak : An algorithm for pulse detection and frequency analysis in hormonal time series

The endocrine control of the reproductive function is often studied from the analysis of luteinizing hormone (LH) pulsatile secretion by the pituitary gland. Whereas measurements in the cavernous sinus cumulate anatomical and technical difficulties, LH levels can be easily assessed from jugular blood. However, plasma levels result from a convolution process due to clearance effects when LH enters the general circulation. Simultaneous measurements comparing LH levels in the cavernous sinus and jugular blood have revealed clear differences in the pulse shape, the amplitude and the baseline. Besides, experimental sampling occurs at a relatively low frequency (typically every 10 min) with respect to LH highest frequency release (one pulse per hour) and the resulting LH measurements are noised by both experimental and assay errors. As a result, the pattern of plasma LH may be not so clearly pulsatile. Yet, reliable information on the InterPulse Intervals (IPI) is a prerequisite to study precisely the steroid feedback exerted on the pituitary level. Hence, there is a real need for robust IPI detection algorithms. In this article, we present an algorithm for the monitoring of LH pulse frequency, basing ourselves both on the available endocrinological knowledge on LH pulse (shape and duration with respect to the frequency regime) and synthetic LH data generated by a simple model. We make use of synthetic data to make clear some basic notions underlying our algorithmic choices. We focus on explaining how the process of sampling affects drastically the original pattern of secretion, and especially the amplitude of the detectable pulses. We then describe the algorithm in details and perform it on different sets of both synthetic and experimental LH time series. We further comment on how to diagnose possible outliers from the series of IPIs which is the main output of the algorithm.Comment: Nombre de pages : 35 ; Nombre de figures : 16 ; Nombre de tableaux :