Towards many colors in FISH on 3D-preserved interphase nuclei

The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process. We discuss (1) M-FISH (combinatorial labeling + deconvolution + widefield microscopy); (2) multicolor labeling + SIM (structured illumination microscopy); (3) the standard approach to multicolor FISH + CLSM (confocal laser scanning microscopy; one fluorochrome - one color channel); (4) combinatorial labeling + CLSM; (5) non-combinatorial labeling + CLSM + linear unmixing. Two related issues, deconvolution of images acquired with CLSM and correction of data for chromatic Z-shift, are also discussed. All methods are illustrated with practical examples. Finally, several rules of thumb helping to choose an optimal labeling + microscopy combination for the planned experiment are suggested. Copyright (c) 2006 S. Karger AG, Basel

Criteria for the differentiation between young and old Onchocerca volvulus filariae

Drugs exist that show long-lasting inhibition of embryogenesis and microfilaria production or macrofilaricidal activity against Onchocerca volvulus. Therefore, the patients have to be followed-up for several years. Clinical drug trials have to be performed in areas with ongoing transmission to assess the efficacy on younger worms. In addition, future vaccine trials may also require demonstrating efficacy against establishment of new worms. For the evaluation of the efficacy, it is necessary to differentiate between older worms, which were exposed to the drug, and younger worms newly acquired after drug treatment or vaccination. Here, we describe criteria for the differentiation between young and old filariae based on histological studies of worms with a known age from travellers, or from children, or patients living in areas with interrupted transmission in Burkina Faso, Ghana or Uganda. Older worms were larger and presented degenerated tissues. Gomori's iron stain showed that the worms accumulated more iron with increasing age, first in the gut and later in other organs. Using an antibody against O. volvulus lysosomal aspartic protease, the gut of young worms was stained only weakly; whereas, it was stronger labelled in older worms, accompanied by additional staining of hypodermis and epithelia. Using morphological and immunohistological criteria, it was possible to differentiate young (1–3 years old) from older females and to identify young males

Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II

The C-terminal domain (CTD) of mammalian RNA polymerase II consists of 52 repeats of the consensus hepta-peptide YSPTSPS, and links transcription to the processing of pre-mRNA. Although Pol II with a CTD shortened to five repeats (Pol II Δ5) is transcriptionally inactive on chromatin templates, it is not clear whether CTD is required for promoter recognition in vivo. Here, we demonstrate that in the context of chromatin, Pol II Δ5 can bind to the c-myc promoter with the same efficiency as wild type Pol II. However, Pol II Δ5 does not form a stable initiation complex, and does not transcribe promoter proximal sequences. Fluorescence recovery after photobleaching (FRAP) experiments with cells expressing enhanced green fluorescent protein (EGFP)-tagged Δ5 or wildtype Pol II revealed a single, highly mobile Pol II Δ5 fraction whereas wildtype Pol II yielded less mobile fractions. These data suggest that CTD is not required for promoter recognition, but rather for subsequent formation of a stable initiation complex and isomerization to an elongation competent complex

Spin squeezing, entanglement and quantum metrology with Bose-Einstein condensates

Squeezed states, a special kind of entangled states, are known as a useful resource for quantum metrology. In interferometric sensors they allow to overcome the "classical" projection noise limit stemming from the independent nature of the individual photons or atoms within the interferometer. Motivated by the potential impact on metrology as wells as by fundamental questions in the context of entanglement, a lot of theoretical and experimental effort has been made to study squeezed states. The first squeezed states useful for quantum enhanced metrology have been proposed and generated in quantum optics, where the squeezed variables are the coherences of the light field. In this tutorial we focus on spin squeezing in atomic systems. We give an introduction to its concepts and discuss its generation in Bose-Einstein condensates. We discuss in detail the experimental requirements necessary for the generation and direct detection of coherent spin squeezing. Two exemplary experiments demonstrating adiabatically prepared spin squeezing based on motional degrees of freedom and diabatically realized spin squeezing based on internal hyperfine degrees of freedom are discussed.Comment: Phd tutorial, 23 pages, 17 figure

Two-dimensional loosely and tightly bound solitons in optical lattices and inverted traps

We study the dynamics of nonlinear localized excitations (solitons) in two-dimensional (2D) Bose-Einstein condensates (BECs) with repulsive interactions, loaded into an optical lattice (OL), which is combined with an external parabolic potential. First, we demonstrate analytically that a broad (loosely bound, LB) soliton state, based on a 2D Bloch function near the edge of the Brillouin zone (BZ), has a negative effective mass (while the mass of a localized state is positive near the BZ center). The negative-mass soliton cannot be held by the usual trap, but it is safely confined by an inverted parabolic potential (anti-trap). Direct simulations demonstrate that the LB solitons (including the ones with intrinsic vorticity) are stable and can freely move on top of the OL. The frequency of elliptic motion of the LB-soliton's center in the anti-trapping potential is very close to the analytical prediction which treats the solition as a quasi-particle. In addition, the LB soliton of the vortex type features real rotation around its center. We also find an abrupt transition, which occurs with the increase of the number of atoms, from the negative-mass LB states to tightly bound (TB) solitons. An estimate demonstrates that, for the zero-vorticity states, the transition occurs when the number of atoms attains a critical number N=10^3, while for the vortex the transition takes place at N=5x10^3 atoms. The positive-mass LB states constructed near the BZ center (including vortices) can move freely too. The effects predicted for BECs also apply to optical spatial solitons in bulk photonic crystals.Comment: 17 pages, 12 figure

Dynamics of Dipolar Spinor Condensates

We study the semiclassical dynamics of a spinor condensate with the magnetic dipole-dipole interaction included. The time evolution of the population imbalance and the relative phase among different spin components depends greatly on the relative strength of interactions as well as on the initial conditions. The interplay of spin exchange and dipole-dipole interaction makes it possible to manipulate the atomic population on different components, leading to the phenomena of spontaneous magnetization and Macroscopic Quantum Self Trapping. Simple estimate demonstrates that these effects are accessible and controllable by modifying the geometry of the trapping potential.Comment: 13 pages,3 figure

Dynamics of positive- and negative-mass solitons in optical lattices and inverted traps

We study the dynamics of one-dimensional solitons in the attractive and repulsive Bose-Einstein condensates (BECs) loaded into an optical lattice (OL), which is combined with an external parabolic potential. First, we demonstrate analytically that, in the repulsive BEC, where the soliton is of the gap type, its effective mass is \emph{negative}. This gives rise to a prediction for the experiment: such a soliton cannot be not held by the usual parabolic trap, but it can be captured (performing harmonic oscillations) by an anti-trapping inverted parabolic potential. We also study the motion of the soliton a in long system, concluding that, in the cases of both the positive and negative mass, it moves freely, provided that its amplitude is below a certain critical value; above it, the soliton's velocity decreases due to the interaction with the OL. At a late stage, the damped motion becomes chaotic. We also investigate the evolution of a two-soliton pulse in the attractive model. The pulse generates a persistent breather, if its amplitude is not too large; otherwise, fusion into a single fundamental soliton takes place. Collisions between two solitons captured in the parabolic trap or anti-trap are considered too. Depending on their amplitudes and phase difference, the solitons either perform stable oscillations, colliding indefinitely many times, or merge into a single soliton. Effects reported in this work for BECs can also be formulated for optical solitons in nonlinear photonic crystals. In particular, the capture of the negative-mass soliton in the anti-trap implies that a bright optical soliton in a self-defocusing medium with a periodic structure of the refractive index may be stable in an anti-waveguide.Comment: 22pages, 9 figures, submitted to Journal of Physics

Classical dynamics of a two-species Bose-Einstein condensate in the presence of nonlinear maser processes

The stability analysis of a generalized Dicke model, in the semi-classical limit, describing the interaction of a two-species Bose-Einstein condensate driven by a quantized field in the presence of Kerr and spontaneous parametric processes is presented. The transitions from Rabi to Josephson dynamics are identified depending on the relative value of the involved parameters. Symmetry-breaking dynamics are shown for both types of coherent oscillations due to the quantized field and nonlinear optical processes.Comment: 12 pages, 5 figures. Accepted for publication as chapter in "Spontaneous Symmetry Breaking, Self-Trapping, and Josephson Oscillations in Nonlinear Systems