A proposed mechanism for IS607-family serine transposases

Background The transposases encoded by the IS607 family of mobile elements are unusual serine recombinases with an inverted domain order and minimal specificity for target DNA.<p></p> Results Structural genomics groups have determined three crystal structures of the catalytic domains of IS607 family transposases. The dimers formed by these catalytic domains are very different from those seen for other serine recombinases and include interactions that usually only occur upon formation of a synaptic tetramer.<p></p> Conclusions Based on these structures, we propose a model for how IS607-family transposases could form a synaptic tetramer. The model suggests that, unlike other serine recombinases, these enzymes carry out sequence-specific DNA binding and catalysis in trans: the DNA binding and catalytic domains of each subunit are proposed to interact with different DNA duplexes. The model also suggests an explanation for the minimal target DNA specificity.<p></p&gt

Andreev scattering in the asymmetric ladder with preformed bosonic pairs

We discuss the phase coherence which emanates from the ladder-like proximity effect between a ``weak superconductor'' with preformed bosonic pairs (here, a single-chain Luther-Emery liquid with superconducting correlations that decay approximately as $x^{-1}$) and a Fermi gas with unpaired fermions. Carefully studying tunneling mechanism(s), we show that the boson-mediated Cooper pairing between remaining unpaired electrons results in a quasi long-range superconductivity: Superconducting correlations decay very slowly as $x^{-\eta}$ with $\eta\approx 1/2$. This process is reminiscent of the coupling of fermions to preformed bosonic pairs introduced in the context of high-Tc cuprates.Comment: 5 pages, final version (To appear in PRB Rapid Communication

The protein-protein interactions required for assembly of the Tn3 resolution synapse

The site‐specific recombinase Tn3 resolvase initiates DNA strand exchange when two res recombination sites and six resolvase dimers interact to form a synapse. The detailed architecture of this intricate recombination machine remains unclear. We have clarified which of the potential dimer‐dimer interactions are required for synapsis and recombination, using a novel complementation strategy that exploits a previously uncharacterized resolvase from Bartonella bacilliformis (“Bart”). Tn3 and Bart resolvases recognize different DNA motifs, via diverged C‐terminal domains (CTDs). They also differ substantially at N‐terminal domain (NTD) surfaces involved in dimerization and synapse assembly. We designed NTD‐CTD hybrid proteins, and hybrid res sites containing both Tn3 and Bart dimer binding sites. Using these components in in vivo assays, we demonstrate that productive synapsis requires a specific “R ” interface involving resolvase NTDs at all three dimer‐binding sites in res . Synapses containing mixtures of wild‐type Tn3 and Bart resolvase NTD dimers are recombination‐defective, but activity can be restored by replacing patches of Tn3 resolvase R interface residues with Bart residues, or vice versa . We conclude that the Tn3 /Bart family synapse is assembled exclusively by R interactions between resolvase dimers, except for the one special dimer‐dimer interaction required for catalysis

Clinical investigation of an outbreak of alveolitis and asthma in a car engine manufacturing plant

Background Exposure to metal working fluid (MWF) has been associated with outbreaks of EAA in the US, with bacterial contamination of MWF being a possible cause, but was uncommon in the UK. Twelve workers developed extrinsic allergic alveolitis (EAA) in a car engine manufacturing plant in the UK, presenting clinically between December 2003 and May 2004. This paper reports the subsequent epidemiological investigation of the whole workforce. This had three aims:- • To measure the extent of the outbreak by identifying other workers who may have developed EAA or other work-related respiratory diseases. • To provide case-detection so that those affected can be treated. • To provide epidemiological data to identify the cause of the outbreak. Methods The outbreak was investigated in a three-phase cross-sectional survey of the workforce. Phase I A respiratory screening questionnaire was completed by 808/836 workers (96.7%) in May 2004. Phase II 481 employees with at least one respiratory symptom on screening and 50 asymptomatic controls were invited for investigation at the factory in June 2004. This included a questionnaire, spirometry and clinical opinion. 454/481(94.4%) responded along with 48/50(96%) controls. Workers were identified who needed further investigation and serial measurements of peak expiratory flow (PEF). Phase III 162 employees were seen at the Birmingham Occupational Lung Disease clinic. 198 employees returned PEF records, including 141 of the 162 who attended for clinical investigation. Case definitions for diagnoses were agreed. Results 87 workers (10.4% of workforce) met case definitions for occupational lung disease, comprising EAA(19), occupational asthma(74) and humidifier fever(7). 12 workers had more than one diagnosis. The peak onset of work-related breathlessness was Spring 2003. The proportion of workers affected was higher for those using metal working fluid (MWF) from a large sump(27.3%) compared with working all over the manufacturing area (7.9%) (OR=4.39,p<0.001). Two workers had positive specific provocation tests to the used but not the unused MWF solution. Conclusions Extensive investigation of the outbreak of EAA detected a large number of affected workers, not only with EAA but also occupational asthma. This is the largest reported outbreak in Europe. Mist from used MWF is the likely cause. In workplaces using MWF, there is a need to carry out risk assessments, to monitor and maintain fluid quality, to control mist and to carry out respiratory health surveillance

Quantum critical point in a periodic Anderson model

We investigate the symmetric Periodic Anderson Model (PAM) on a three-dimensional cubic lattice with nearest-neighbor hopping and hybridization matrix elements. Using Gutzwiller's variational method and the Hubbard-III approximation (which corresponds to the exact solution of an appropriate Falicov-Kimball model in infinite dimensions) we demonstrate the existence of a quantum critical point at zero temperature. Below a critical value $V_c$ of the hybridization (or above a critical interaction $U_c$) the system is an {\em insulator} in Gutzwiller's and a {\em semi-metal} in Hubbard's approach, whereas above $V_c$ (below $U_c$) it behaves like a metal in both approximations. These predictions are compared with the density of states of the $d$- and $f$-bands calculated from Quantum Monte Carlo and NRG calculations. Our conclusion is that the half-filled symmetric PAM contains a {\em metal-semimetal transition}, not a metal-insulator transition as has been suggested previously.Comment: ReVteX, 10 pages, 2 EPS figures. Minor corrections made in the text and in the figure captions from the first version. More references added. Accepted for publication in Physical Review

Two-particle pairing and phase separation in a two-dimensional Bose-gas with one or two sorts of bosons

We present a phase diagram for a dilute two-dimensional Bose-gas on a lattice. For one sort of boson we consider a realistic case of the van der Waals interaction between particles with a strong hard-core repulsion $U$ and a van der Waals attractive tail $V$. For $V< 2 t$, $t$ being a hopping amplitude, the phase diagram of the system contains regions of the usual one-particle Bose-Einstein condensation (BEC). However for $V>2t$ we have total phase separation on a Mott-Hubbard Bose solid and a dilute Bose gas. For two sorts of structureless bosons described by the two band Hubbard model an s-wave pairing of the two bosons of different sort $\neq 0$ is possible. The results we obtained should be important for different Bose systems, including submonolayers of $^4$He, excitons in semiconductors, Schwinger bosons in magnetic systems and holons in HTSC. In the HTSC case a possibility of two-holon pairing in the slave-bosons theories of superconductivity can restore a required charge $2e$ of a Cooper pair.Comment: 10 pages, 2 figure

Origin of strange metallic phase in cuprate superconductors

The origin of strange metallic phase is shown to exist due to these two conditions---(i) the electrons are strongly interacting such that there are no band and Mott-Hubbard gaps, and (ii) the electronic energy levels are crossed in such a way that there is an electronic energy gap between two energy levels associated to two different wave functions. The theory is also exploited to explain (i) the upward- and downward-shifts in the $T$-linear resistivity curves, and (ii) the spectral weight transfer observed in the soft X-ray absorption spectroscopic measurements of the La-Sr-Cu-O Mott insulator.Comment: To be published in J. Supercond. Nov. Mag

Nonlinear electrodynamics of p-wave superconductors

We consider the Maxwell-London electrodynamics of three dimensional superconductors in p-wave pairing states with nodal points or lines in the energy gap. The current-velocity relation is then nonlinear in the applied field, cubic for point nodes and quadratic for lines. We obtain explicit angular and depth dependent expressions for measurable quantities such as the transverse magnetic moment, and associated torque. These dependences are different for point and line nodes and can be used to distinguish between different order parameters. We discuss the experimental feasibility of this method, and bring forth its advantages, as well as limitations that might be present.Comment: Fourteen pages RevTex plus four postscript figure

Multi-Channel Kondo Necklace

A multi--channel generalization of Doniach's Kondo necklace model is formulated, and its phase diagram studied in the mean--field approximation. Our intention is to introduce the possible simplest model which displays some of the features expected from the overscreened Kondo lattice. The $N$ conduction electron channels are represented by $N$ sets of pseudospins \vt_{j}, $j=1, ... , N$, which are all antiferromagnetically coupled to a periodic array of |\vs|=1/2 spins. Exploiting permutation symmetry in the channel index $j$ allows us to write down the self--consistency equation for general $N$. For $N>2$, we find that the critical temperature is rising with increasing Kondo interaction; we interpret this effect by pointing out that the Kondo coupling creates the composite pseudospin objects which undergo an ordering transition. The relevance of our findings to the underlying fermionic multi--channel problem is discussed.Comment: 29 pages (2 figures upon request from [email protected]), LATEX, submitted for publicatio

Three-Particle Correlations in Simple Liquids

We use video microscopy to follow the phase-space trajectory of a two-dimensional colloidal model liquid and calculate three-point correlation functions from the measured particle configurations. Approaching the fluid-solid transition by increasing the strength of the pair-interaction potential, one observes the gradual formation of a crystal-like local order due to triplet correlations, while being still deep inside the fluid phase. Furthermore, we show that in a strongly interacting system the Born-Green equation can be satisfied only with the full triplet correlation function but not with three-body distribution functions obtained from superposing pair-correlations (Kirkwood superposition approximation).Comment: 4 pages, submitted to PRL, experimental paper, 2nd version: Fig.1 and two new paragraphs have been adde