Inhibitory Receptor Signaling Destabilizes Immunological Synapse Formation in Primary NK Cells

Upon engagement of their cognate class I major histocompatibility complex ligands, receptors containing immunotyrosine-based inhibitory motifs (ITIMs) transduce signals that block cytolytic and inflammatory responses. In this manner, ITIM-coupled receptors play a crucial role in maintaining natural killer (NK) cell tolerance toward normal, healthy tissue. A number of studies, mostly using immortalized NK cell lines, have demonstrated that ITIM signaling functions by disrupting the cytolytic immunological synapse formed between an NK cell and its target. However, more recent imaging experiments using primary NK cells have suggested that inhibitory receptor engagement does not antagonize contact formation, casting doubt on the hypothesis that ITIM signals destabilize the synapse. To resolve this issue, we analyzed primary NK cell activation and contact formation on supported lipid bilayers containing controlled combinations of activating and inhibitory ligands. Under these conditions, we observed that ITIM signaling clearly inhibited adhesion, cell arrest, and calcium influx, three hallmarks of synapse formation. These results are consistent with previous reports showing that inhibitory receptors deliver a “reverse stop” signal, and confirm that ITIM signaling functions at least in part by destabilizing cytolytic synapse formation

Crystal Structure of the Cytoplasmic Domain of the Type I TGF β Receptor in Complex with FKBP12

AbstractActivation of the type I TGF β receptor (T β R-I) requires phosphorylation of a regulatory segment known as the GS region, located upstream of the serine/threonine kinase domain in the cytoplasmic portion of the receptor. The crystal structure of a fragment of unphosphorylated T β R-I, containing both the GS region and the catalytic domain, has been determined in complex with the FK506-binding protein FKBP12. T β R-I adopts an inactive conformation that is maintained by the unphosphorylated GS region. FKBP12 binds to the GS region of the receptor, capping the T β R-II phosphorylation sites and further stabilizing the inactive conformation of T β R-I. Certain structural features at the catalytic center of T β R-I are characteristic of tyrosine kinases rather than Ser/Thr kinases

Feshbach resonance in a strictly two-dimensional atomic Bose gas

We discuss the atom-atom scattering problem across a Feshbach resonance in a two-dimensional dilute Bose gas at zero temperature, in the limit where the s-wave scattering length exceeds the width of the vertical confinement. We determine a tunable coupling-strength parameter and by controlling it we evaluate how the condensate wave function spreads out with increasing atom-atom repulsions. We also discuss the stability of the condensate in the magnetic-field regime where the coupling has become attractive.Comment: 9 pages, 1 figur

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Beyond Gross-Pitaevskii Mean Field Theory

A large number of effects related to the phenomenon of Bose-Einstein Condensation (BEC) can be understood in terms of lowest order mean field theory, whereby the entire system is assumed to be condensed, with thermal and quantum fluctuations completely ignored. Such a treatment leads to the Gross-Pitaevskii Equation (GPE) used extensively throughout this book. Although this theory works remarkably well for a broad range of experimental parameters, a more complete treatment is required for understanding various experiments, including experiments with solitons and vortices. Such treatments should include the dynamical coupling of the condensate to the thermal cloud, the effect of dimensionality, the role of quantum fluctuations, and should also describe the critical regime, including the process of condensate formation. The aim of this Chapter is to give a brief but insightful overview of various recent theories, which extend beyond the GPE. To keep the discussion brief, only the main notions and conclusions will be presented. This Chapter generalizes the presentation of Chapter 1, by explicitly maintaining fluctuations around the condensate order parameter. While the theoretical arguments outlined here are generic, the emphasis is on approaches suitable for describing single weakly-interacting atomic Bose gases in harmonic traps. Interesting effects arising when condensates are trapped in double-well potentials and optical lattices, as well as the cases of spinor condensates, and atomic-molecular coupling, along with the modified or alternative theories needed to describe them, will not be covered here.Comment: Review Article (19 Pages) - To appear in 'Emergent Nonlinear Phenomena in Bose-Einstein Condensates: Theory and Experiment', Edited by P.G. Kevrekidis, D.J. Frantzeskakis and R. Carretero-Gonzalez (Springer Verlag

CPEB2, CPEB3 and CPEB4 are coordinately regulated by miRNAs recognizing conserved binding sites in paralog positions of their 3′-UTRs

The cytoplasmic polyadenylation element binding-protein (CPEB) is an RNA-binding protein that participates in translational control. CPEB2, CPEB3 and CPEB4 are paralog proteins very similar among themselves referred as the CPEB2 subfamily. To gain insight into common mechanisms of regulation of the CPEB2 subfamily transcripts, we looked for putative cis-acting elements present in the 3′-UTRs of the three paralogs. We found different families of miRNAs predicted to target all subfamily members. Most predicted target sites for these families are located in paralog positions suggesting that these putative regulatory motifs were already present in the ancestral gene. We validated target sites for miR-92 and miR-26 in the three paralogs using mutagenesis of miRNA-binding sites in reporter constructs combined with over-expression and depletion of miRNAs. Both miR-92 and miR-26 induced a decrease in Luciferase activity associated to a reduction in mRNA levels of the reporter constructs. We also showed that the endogenous miRNAs co-regulate CPEB2, CPEB3 and CPEB4 transcripts, supporting our hypothesis that these genes have a common regulatory mechanism mediated by miRNAs. We also suggest that the ancestral pattern of miRNA-binding motifs was maintained throughout the generation of highly conserved elements in each of the 3′-UTRs

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE

Evaluating the suitability of coupled biophysical models for fishery management

The potential role of coupled biophysical models in enhancing the conservation, management, and recovery of fish stocks is assessed, with emphasis on anchovy, cod, herring, and sprat in European waters. The assessment indicates that coupled biophysical models are currently capable of simulating transport patterns, along with temperature and prey fields within marine ecosystems; they therefore provide insight into the variability of early-life-stage dynamics and connectivity within stocks. Moreover, the influence of environmental variability on potential recruitment success may be discerned from model hindcasts. Based on case studies, biophysical modelling results are shown to be capable of shedding light on whether stock management frameworks need re-evaluation. Hence, key modelling products were identified that will contribute to the development of viable stock recovery plans and management strategies. The study also suggests that approaches combining observation, process knowledge, and numerical modelling could be a promising way forward in understanding and simulating the dynamics of marine fish populations

Theory of Bose-Einstein condensation in trapped gases

The phenomenon of Bose-Einstein condensation of dilute gases in traps is reviewed from a theoretical perspective. Mean-field theory provides a framework to understand the main features of the condensation and the role of interactions between particles. Various properties of these systems are discussed, including the density profiles and the energy of the ground state configurations, the collective oscillations and the dynamics of the expansion, the condensate fraction and the thermodynamic functions. The thermodynamic limit exhibits a scaling behavior in the relevant length and energy scales. Despite the dilute nature of the gases, interactions profoundly modify the static as well as the dynamic properties of the system; the predictions of mean-field theory are in excellent agreement with available experimental results. Effects of superfluidity including the existence of quantized vortices and the reduction of the moment of inertia are discussed, as well as the consequences of coherence such as the Josephson effect and interference phenomena. The review also assesses the accuracy and limitations of the mean-field approach.Comment: revtex, 69 pages, 38 eps figures, new version with more references, new figures, various changes and corrections, for publ. in Rev. Mod. Phys., available also at http://www-phys.science.unitn.it/bec/BEC.htm