Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci

Background: A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells, and explored the spatio-temporal process of Barr body formation at onset of inactivation in early differentiating mouse embryonic stem cells (ESCs). Results: We demonstrate that all CTs are composed of structurally linked chromatin domain clusters (CDCs). In active CTs the periphery of CDCs harbors low-density chromatin enriched with transcriptionally competent markers, called the perichromatin region (PR). The PR borders on a contiguous channel system, the interchromatin compartment (IC), which starts at nuclear pores and pervades CTs. We propose that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC). The Barr body differs from active CTs by a partially collapsed ANC with CDCs coming significantly closer together, although a rudimentary IC channel system connected to nuclear pores is maintained. Distinct Xist RNA foci, closely adjacent to the nuclear matrix scaffold attachment factor-A (SAF-A) localize throughout Xi along the rudimentary ANC. In early differentiating ESCs initial Xist RNA spreading precedes Barr body formation, which occurs concurrent with the subsequent exclusion of RNA polymerase II (RNAP II). Induction of a transgenic autosomal Xist RNA in a male ESC triggers the formation of an `autosomal Barr body' with less compacted chromatin and incomplete RNAP II exclusion. Conclusions: 3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body. Basic structural features of CT organization such as CDCs and IC channels are however still recognized, arguing against a uniform compaction of the Barr body at the nucleosome level. The localization of distinct Xist RNA foci at boundaries of the rudimentary ANC may be considered as snap-shots of a dynamic interaction with silenced genes. Enrichment of SAF-A within Xi territories and its close spatial association with Xist RNA suggests their cooperative function for structural organization of Xi

Nonlinear Periodic Phononic Structures and Granular Crystals

This chapter describes the dynamic behavior of nonlinear periodic phononic structures, along with how such structures can be utilized to affect the propagation of mechanical waves. Granular crystals are one type of nonlinear periodic phononic structure and are the focus of this chapter. The chapter begins with a brief history of nonlinear lattices and an introduction to granular crystals. This is followed by a summary of past and recent work on one-dimensional (1D) and two-dimensional (2D) granular crystals, which is categorized according to the crystals’ periodicity and dynamical regime. The chapter is concluded with a commentary by the authors, which discusses several possible future directions relating to granular crystals and other nonlinear periodic phononic structures. Throughout this chapter, a richness of nonlinear dynamic effects that occur in granular crystals is revealed, including a plethora of phenomena with no linear analog such as solitary waves, discrete breathers, tunable frequency band gaps, bifurcations, and chaos. Furthermore, in addition to the description of fundamental nonlinear phenomena, the authors describe how such phenomena can enable novel engineering devices and be applied to other nonlinear periodic systems

Modulation of immune responses by targeting CD169/Siglec-1 with the glycan ligand

A fundamental role in the plant-bacterium interaction for Gram-negative phytopathogenic bacteria is played by membrane constituents, such as proteins, lipopoly- or lipooligosaccharides (LPS, LOS) and Capsule Polysaccharides (CPS). In the frame of the understanding the molecular basis of plant bacterium interaction, the Gram-negative bacterium Agrobacterium vitis was selected in this study. It is a phytopathogenic member of the Rhizobiaceae family and it induces the crown gall disease selectively on grapevines (Vitis vinifera). A. vitis wild type strain F2/5, and its mutant in the quorum sensing gene ΔaviR, were studied. The wild type produces biosurfactants; it is considered a model to study surface motility, and it causes necrosis on grapevine roots and HR (Hypersensitive Response) on tobacco. Conversely, the mutant does not show any surface motility and does not produce any surfactant material; additionally, it induces neither necrosis on grape, nor HR on tobacco. Therefore, the two strains were analyzed to shed some light on the QS regulation of LOS structure and the consequent variation, if any, on HR response. LOS from both strains were isolated and characterized: the two LOS structures maintained several common features and differed for few others. With regards to the common patterns, firstly: the Lipid A region was not phosphorylated at C4 of the non reducing glucosamine but glycosylated by an uronic acid (GalA) unit, secondly: a third Kdo and the rare Dha (3-deoxy-lyxo-2-heptulosaric acid) moiety was present. Importantly, the third Kdo and the Dha residues were substituted by rhamnose in a not stoichiometric fashion, giving four different oligosaccharide species. The proportions among these four species, is the key difference between the LOSs from both the two bacteria. LOS from both strains and Lipid A from wild type A. vitis are now examined for their HR potential in tobacco leaves and grapevine roots