Joining of Immunoglobulin Heavy Chain Gene Segments: Implications from a Chromosome with Evidence of Three D-JH Fusions

A chromosomal segment with a unique structure around the immunoglobulin heavy chain joining region (JH) has been molecularly cloned from an Abelson murine leukemia virus-transformed cell line. Attached to JH3 in the cloned DNA, in inverted sequence, is the DNA from JH1 to the JH2 recognition sequence. The inverted segment is attached at its other end to the 5' recognition sequence of a diversity segment (D). To form this structure, three joining events must have occurred on the same chromosome. One of these events could have been a normal D-JH joining but the others must have been irregular events including ones that result in inversions. One of the joining events left fused recognition elements from JH2 and a D whose sequence shows that, during joining, reciprocal joinings of the recognition elements must occur to fuse the heptameric elements back to back. Because joined D and JH undergo deletion of terminal coding sequence during recombination but the joined heptameric recognition sequences do not contain the deleted sequence, joining must be a nonreciprocal event. Also, extra nucleotides are inserted between D and JH as part of the joining process; it is suggested that this added sequence is a product of the activity of terminal deoxynucleotidyltransferase at the D/JH (and probably the VH/D) joints and that it represents a new element of heavy chain gene structure, the N region

Precision preparation of strings of trapped neutral atoms

We have recently demonstrated the creation of regular strings of neutral caesium atoms in a standing wave optical dipole trap using optical tweezers [Y. Miroshnychenko et al., Nature, in press (2006)]. The rearrangement is realized atom-by-atom, extracting an atom and re-inserting it at the desired position with sub-micrometer resolution. We describe our experimental setup and present detailed measurements as well as simple analytical models for the resolution of the extraction process, for the precision of the insertion, and for heating processes. We compare two different methods of insertion, one of which permits the placement of two atoms into one optical micropotential. The theoretical models largely explain our experimental results and allow us to identify the main limiting factors for the precision and efficiency of the manipulations. Strategies for future improvements are discussed.Comment: 25 pages, 18 figure

Three charged particles in the continuum. Astrophysical examples

We suggest a new adiabatic approach for description of three charged particles in the continuum. This approach is based on the Coulomb-Fourier transformation (CFT) of three body Hamiltonian, which allows to develop a scheme, alternative to Born-Oppenheimer one. The approach appears as an expansion of the kernels of corresponding integral transformations in terms of small mass-ratio parameter. To be specific, the results are presented for the system $ppe$ in the continuum. The wave function of a such system is compared with that one which is used for estimation of the rate for triple reaction $p+p+e\to d+\nu,$ which take place as a step of $pp$-cycle in the center of the Sun. The problem of microscopic screening for this particular reaction is discussed

Molecular basis of heavy-chain class switching and switch region deletion in an Abelson virus-transformed cell line

We demonstrated that a subclone of an Abelson murine leukemia virus-transformed B-lymphoid cell line switched from mu to gamma 2b expression in vitro, by the classical recombination-deletion mechanism. In this line, the expressed VHDJH region and the C gamma 2b constant region gene were juxtaposed by a recombination event which linked the highly repetitive portions of the S mu and S gama 2b regions and resulted in the loss of the C mu gene from the intervening region. An additional recombination event in this subclone involved an internal deletion in the S mu region of the expressed (switched) allele. One end of this deletion occurred very close to the switch recombination point. Despite the recombination-deletion mechanism of switching, the gamma 2b-producing line retained two copies of the C mu gene and two copies of the sequence just 5' to the S gamma 2b recombination point. The possible significance of the retention of these sequences to the mechanism of class switching is discussed

A parabolic free boundary problem with Bernoulli type condition on the free boundary

Consider the parabolic free boundary problem $$\Delta u - \partial_t u = 0 \textrm{in} \{u>0\}, |\nabla u|=1 \textrm{on} \partial\{u>0\} .$$ For a realistic class of solutions, containing for example {\em all} limits of the singular perturbation problem $$\Delta u_\epsilon - \partial_t u_\epsilon = \beta_\epsilon(u_\epsilon) \textrm{as} \epsilon\to 0,$$ we prove that one-sided flatness of the free boundary implies regularity. In particular, we show that the topological free boundary $\partial\{u>0\}$ can be decomposed into an {\em open} regular set (relative to $\partial\{u>0\}$) which is locally a surface with H\"older-continuous space normal, and a closed singular set. Our result extends the main theorem in the paper by H.W. Alt-L.A. Caffarelli (1981) to more general solutions as well as the time-dependent case. Our proof uses methods developed in H.W. Alt-L.A. Caffarelli (1981), however we replace the core of that paper, which relies on non-positive mean curvature at singular points, by an argument based on scaling discrepancies, which promises to be applicable to more general free boundary or free discontinuity problems

Three- and Four-Body Scattering Calculations including the Coulomb Force

The method of screening and renormalization for including the Coulomb interaction in the framework of momentum-space integral equations is applied to the three- and four-body nuclear reactions. The Coulomb effect on the observables and the ability of the present nuclear potential models to describe the experimental data is discussed.Comment: Proceedings of the Critical Stability workshop, Erice, Sicily, October 2008, to be published in Few-Body System

Coherence properties and quantum state transportation in an optical conveyor belt

We have prepared and detected quantum coherences with long dephasing times at the level of single trapped cesium atoms. Controlled transport by an "optical conveyor belt" over macroscopic distances preserves the atomic coherence with slight reduction of coherence time. The limiting dephasing effects are experimentally identified and are of technical rather than fundamental nature. We present an analytical model of the reversible and irreversible dephasing mechanisms. Coherent quantum bit operations along with quantum state transport open the route towards a "quantum shift register" of individual neutral atoms.Comment: 4 pages, 3 figure

A neutral atom quantum register

We demonstrate the realization of a quantum register using a string of single neutral atoms which are trapped in an optical dipole trap. The atoms are selectively and coherently manipulated in a magnetic field gradient using microwave radiation. Our addressing scheme operates with a high spatial resolution and qubit rotations on individual atoms are performed with 99% contrast. In a final read-out operation we analyze each individual atomic state. Finally, we have measured the coherence time and identified the predominant dephasing mechanism for our register.Comment: 4 pages, 4 figure

Adiabatic Quantum State Manipulation of Single Trapped Atoms

We use microwave induced adiabatic passages for selective spin flips within a string of optically trapped individual neutral Cs atoms. We position-dependently shift the atomic transition frequency with a magnetic field gradient. To flip the spin of a selected atom, we optically measure its position and sweep the microwave frequency across its respective resonance frequency. We analyze the addressing resolution and the experimental robustness of this scheme. Furthermore, we show that adiabatic spin flips can also be induced with a fixed microwave frequency by deterministically transporting the atoms across the position of resonance.Comment: 4 pages, 4 figure