Tunneling Conductance Between Parallel Two Dimensional Electron Systems

We derive and evaluate expressions for the low temperature {\it dc} equilibrium tunneling conductance between parallel two-dimensional electron systems. Our theory is based on a linear-response formalism and on impurity-averaged perturbation theory. The disorder broadening of features in the dependence of tunneling conductance on sheet densities and in-plane magnetic field strengths is influenced both by the finite lifetime of electrons within the wells and by non-momentum-conserving tunneling events. Disorder vertex corrections are important only for weak in-plane magnetic fields and strong interwell impurity-potential correlations. We comment on the basis of our results on the possibility of using tunneling measurements to determine the lifetime of electrons in the quantum wells.Comment: 14 pages, 5 Fig. not included, revtex, IUcm92-00

Lifetime of Two-Dimensional Electrons Measured by Tunneling Spectroscopy

For electrons tunneling between parallel two-dimensional electron systems, conservation of in-plane momentum produces sharply resonant current-voltage characteristics and provides a uniquely sensitive probe of the underlying electronic spectral functions. We report here the application of this technique to accurate measurements of the temperature dependence of the electron-electron scattering rate in clean two-dimensional systems. Our results are in qualitative agreement with existing calculations.Comment: file in REVTEX format produces 11 pages, 3 figures available from [email protected]

Mesoscopic effects in tunneling between parallel quantum wires

We consider a phase-coherent system of two parallel quantum wires that are coupled via a tunneling barrier of finite length. The usual perturbative treatment of tunneling fails in this case, even in the diffusive limit, once the length L of the coupling region exceeds a characteristic length scale L_t set by tunneling. Exact solution of the scattering problem posed by the extended tunneling barrier allows us to compute tunneling conductances as a function of applied voltage and magnetic field. We take into account charging effects in the quantum wires due to applied voltages and find that these are important for 1D-to-1D tunneling transport.Comment: 8 pages, 7 figures, improved Figs., added Refs. and appendix, to appear in Phys. Rev.

Tunneling Between Two-Dimensional Electron Gases in a Strong Magnetic Field

We have measured the tunneling between two two-dimensional electron gases at high magnetic fields $B$, when the carrier densities of the two electron layers are matched. For filling factors $\nu<1$, there is a gap in the current-voltage characteristics centered about $V=0$, followed by a tunneling peak at $\sim 6$~mV. Both features have been observed before and have been attributed to electron-electron interactions within a layer. We have measured high field tunneling peak positions and fitted gap parameters that are proportional to $B$, and independent of the carrier densities of the two layers. This suggests a different origin for the gap to that proposed by current theories, which predict a $\sqrt{B}$ dependence.Comment: 9 pages, cond-mat/yymmnn

Strategic and practical guidelines for successful structured illumination microscopy

Linear 2D- or 3D-structured illumination microscopy (SIM or3D-SIM, respectively) enables multicolor volumetric imaging of fixed and live specimens with subdiffraction resolution in all spatial dimensions. However, the reliance of SIM on algorithmic post-processing renders it particularly sensitive to artifacts that may reduce resolution, compromise data and its interpretations, and drain resources in terms of money and time spent. Here we present a protocol that allows users to generate high-quality SIM data while accounting and correcting for common artifacts. The protocol details preparation of calibration bead slides designed for SIM-based experiments, the acquisition of calibration data, the documentation of typically encountered SIM artifacts and corrective measures that should be taken to reduce them. It also includes a conceptual overview and checklist for experimental design and calibration decisions, and is applicable to any commercially available or custom platform. This protocol, plus accompanying guidelines, allows researchers from students to imaging professionals to create an optimal SIM imaging environment regardless of specimen type or structure of interest. The calibration sample preparation and system calibration protocol can be executed within 1-2 d

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

Computational geometry analysis of dendritic spines by structured illumination microscopy

We are currently short of methods that can extract objective parameters of dendritic spines useful for their categorization. Authors present in this study an automatic analytical pipeline for spine geometry using 3D-structured illumination microscopy, which can effectively extract many geometrical parameters of dendritic spines without bias and automatically categorize spine population based on their morphological feature

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

Integrating chromatin and development: LDB1 regulates genome architecture and gene expression in motor neuron differentiation

Dynamic changes in chromatin architecture underpin gene expression in development. The chromatin integrator protein LDB1 is a key regulatory node in the organization of developmentally-specific gene expression programs, particularly in motor neurons (MNs) of the vertebrate spinal cord. By coordinating transcription factor binding, chromatin remodeling, and 3D genome organization, LDB1 is an essential chromatin integrator protein in the development of MNs. In this thesis I characterise the deletion of LDB1 in an in vitro MN differentiation system in the mouse. By measuring transcription factor (TF) binding, protein association, gene expression, and 3D-genome organization, I specify the genetic elements that LDB1 regulates. I find that LDB1 regulates binding of the promiscuous TFs Isl1 and Lhx3 at a subset of critical MN genes, specified particularly in cooperation with the LDB1 binding partner SSDP1, where it drives open chromatin, H3K27ac deposition, gene expression, and likely enhancer function. Thus, LDB1 integrates multiple levels of specificity to regulate dozens of genes and enhancers that are critical to the expression of MN genes. I propose that this is a key feature of spatial genome regulation and is mediated by LDB1 and the interaction with its binding partner SSDP1. I identify a minimal set of MN-specific genes regulated by LDB1, as well as a set of elements that regulate subtle features of 3D genome organization and transcription. Together, I establish LDB1 as a critical regulator of 3D genome organization, transcription factor assembly, and gene expression, making LDB1 and genes downstream of its effects into promising targets for improved cellular reprogramming strategies.</p