Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?

DNA-strand exchange is a vital step in the recombination process, of which a key intermediate is the four-way DNA Holliday junction formed transiently in most living organisms. Here, the single-crystal structure at a resolution of 2.35 Å of such a DNA junction formed by d(CCGGTACCGG)2, which has crystallized in a more highly symmetrical packing mode to that previously observed for the same sequence, is presented. In this case, the structure is isomorphous to the mismatch sequence d(CCGGGACCGG)2, which reveals the roles of both lattice and DNA sequence in determining the junction geometry. The helices cross at the larger angle of 43.0° (the previously observed angle for this sequence was 41.4°) as a right-handed X. No metal cations were observed; the crystals were grown in the presence of only group I counter-cations.

The distributed work of local action: interaction amongst virtually collocated research teams

Existing research on synchronous remote working in CSCW has highlighted the troubles that can arise because actions at one site are (partially) unavailable to remote colleagues. Such ‘local action’ is routinely characterised as a nuisance, a distraction, subordinate and the like. This paper explores interconnections between ‘local action’ and ‘distributed work’ in the case of a research team virtually collocated through ‘MiMeG’. MiMeG is an e-Social Science tool that facilitates ‘distributed data sessions’ in which social scientists are able to remotely collaborate on the real-time analysis of video data. The data are visible and controllable in a shared workspace and participants are additionally connected via audio conferencing. The findings reveal that whilst the (partial) unavailability of local action is at times problematic, it is also used as a resource for coordinating work. The paper considers how local action is interactionally managed in distributed data sessions and concludes by outlining implications of the analysis for the design and study of technologies to support group-to-group collaboration.

Where the interaction is: collisions of the situated and mediated in living room interactions

This article presents three ethnographic tales of interactions with living room media to help recreate the experience of significant moments in time, of affective encounters at the interface in which there is a collision or confusion of situated and virtual worlds. It draws on a year-long video ethnography of the practice and performance of everyday interactions with living room media. By studying situated activity and the lived practice of (new) media, rather than taking an exclusive focus on the virtual as a detached space, this ethnographic work demonstrates how the situated and mediated clash, or are crafted into complex emotional encounters during everyday living room life.

Interaction of PPARG Pro12Ala with dietary fat influences plasma lipids in subjects at cardiometabolic risk

The PPARγ2 gene SNP Pro12Ala has shown variable association with metabolic syndrome traits in healthy subjects. We investigated the effect of interaction between genotype and the ratio of polyunsaturated:saturated (P:S) fatty acid intake on plasma lipids in 367 White subjects aged 30-70 y at increased cardiometabolic risk, in the RISCK study. Interaction was determined after habitual diet at recruitment, at baseline after a 4-week high-SFA (HS) diet and after 24-week reference (HS), high-MUFA (HM) and low-fat (LF) diets. At recruitment, there were no significant associations between genotype and plasma lipids, however, P:S x genotype interaction influenced plasma total cholesterol (TC) (P=0.02), LDL-cholesterol (LDL-C) (P=0.002) and triglyceride (TG) (P=0.02) concentrations. At P:S ratio ≤0.33, mean TC and LDL-C concentrations in Ala12 allele carriers were significantly higher than in non-carriers (respectively P=0.003; P=0.0001). Significant trends in reduction of plasma TC (P=0.02) and TG (P=0.002) concentrations occurred with increasing P:S (respectively ≤0.33 to >0.65 and 0.34 to >0.65) in Ala12 allele carriers. There were no significant differences between carriers and non-carriers after the 4-week HS diet or 24-week interventions. Plasma TC and TG concentrations in PPARG Ala12 allele carriers decrease as P:S increases, but are not dependent on a reduction in SFA intake.

DC-SIGN increases the affinity of HIV-1 envelope glycoprotein interaction with CD4

Mannose-binding C-type lectin receptors, expressed on Langerhans cells and subepithelial dendritic cells (DCs) of cervico-vaginal tissues, play an important role in HIV-1 capture and subsequent dissemination to lymph nodes. DC-SIGN has been implicated in both productive infection of DCs and the DC-mediated trans infection of CD4(+) T cells that occurs in the absence of replication. However, the molecular events that underlie this efficient transmission have not been fully defined. In this study, we have examined the effect of the extracellular domains of DC-SIGN and Langerin on the stability of the interaction of the HIV-1 envelope glycoprotein with CD4 and also on replication in permissive cells. Surface plasmon resonance analysis showed that DC-SIGN increases the binding affinity of trimeric gp140 envelope glycoproteins to CD4. In contrast, Langerin had no effect on the stability of the gp140:CD4 complex. In vitro infection experiments to compare DC-SIGN enhancement of CD4-dependent and CD4-independent strains demonstrated significantly lower enhancement of the CD4-independent strain. In addition DC-SIGN increased the relative rate of infection of the CD4-dependent strain but had no effect on the CD4-independent strain. DC-SIGN binding to the HIV envelope protein effectively increases exposure of the CD4 binding site, which in turn contributes to enhancement of infection.

The interaction of flexural-gravity waves with periodic geometries

A periodic structure of finite extent is embedded within an otherwise uniform two-dimensional system consisting of finite-depth fluid covered by a thin elastic plate. An incident harmonic flexural-gravity wave is scattered by the structure. By using an approximation to the corresponding linearised boundary value problem that is based on a slowly varying structure in conjunction with a transfer matrix formulation, a method is developed that generates the whole solution from that for just one cycle of the structure, providing both computational savings and insight into the scattering process. Numerical results show that variations in the plate produce strong resonances about the ‘Bragg frequencies’ for relatively few periods. We find that certain geometrical variations in the plate generate these resonances above the Bragg value, whereas other geometries produce the resonance below the Bragg value. The familiar resonances due to periodic bed undulations tend to be damped by the plate.

A Real-time, Predictive Architecture for Distributed Virtual Reality

User interaction within a virtual environment may take various forms: a teleconferencing application will require users to speak to each other (Geak, 1993), with computer supported co-operative working; an Engineer may wish to pass an object to another user for examination; in a battle field simulation (McDonough, 1992), users might exchange fire. In all cases it is necessary for the actions of one user to be presented to the others sufficiently quickly to allow realistic interaction. In this paper we take a fresh look at the approach of virtual reality operating systems by tackling the underlying issues of creating real-time multi-user environments.

An investigation of the expression and adhesin function of H7 flagella in the interaction of Escherichia coli O157: H7 with bovine intestinal epithelium

Enterohaemorrhagic Escherichia coli O157 : H7 is a bacterial pathogen that can cause haemorrhagic colitis and haemolytic uremic syndrome. In the primary reservoir host, cattle, the terminal rectum is the principal site of E. coli O157 colonization. In this study, bovine terminal rectal primary epithelial cells were used to examine the role of H7 flagella in epithelial adherence. Binding of a fliC(H7) mutant O157 strain to rectal epithelium was significantly reduced as was binding of the flagellated wild-type strain following incubation with H7-specific antibodies. Complementation of fliC(H7) mutant O157 strain with fliC(H7) restored the adherence to wild-type levels; however, complementation with fliC(H6) did not restore it. High-resolution ultrastructural and imunofluorescence studies demonstrated the presence of abundant flagella forming physical contact points with the rectal epithelium. Binding to terminal rectal epithelium was specific to H7 by comparison with other flagellin types tested. In-cell Western assays confirmed temporal expression of flagella during O157 interaction with epithelium, early expression was suppressed during the later stages of microcolony and attaching and effacing lesion formation. H7 flagella are expressed in vivo by individual bacteria in contact with rectal mucosa. Our data demonstrate that the H7 flagellum acts as an adhesin to bovine intestinal epithelium and its involvement in this crucial initiating step for colonization indicates that H7 flagella could be an important target in intervention strategies.

Interaction of enterohemorrhagic Escherichia coli O157 : H7 with mouse intestinal mucosa

In this study, we used mouse ileal loops to investigate the interaction of enterohemorrhagic Escherichia coli (EHEC) O157:H7 with the mouse intestinal mucosa. With a dose of 10(9) and 3 h incubation, EHEC O157 was detected in the lumen and to a lesser extent associated with the epithelium. Typical attaching and effacing (A/E) lesions were seen, albeit infrequently. While the effector protein Tir was essential for A/E lesion formation, the bacterial type III secretion system adaptor protein TccP was dispensable. These results suggest that A/E lesions on mouse intestinal mucosa can be formed independently of robust actin polymerization.

Solvent-dependent modulation of metal–metal electronic interactions in a dinuclear cyanoruthenate complex: a detailed electrochemical, spectroscopic and computational study

The dinuclear complex [{Ru(CN)4}2(μ-bppz)]4− shows a strongly solvent-dependent metal–metal electronic interaction which allows the mixed-valence state to be switched from class 2 to class 3 by changing solvent from water to CH2Cl2. In CH2Cl2 the separation between the successive Ru(II)/Ru(III) redox couples is 350 mVand the IVCT band (from the UV/Vis/NIR spectroelectrochemistry) is characteristic of a borderline class II/III or class III mixed valence state. In water, the redox separation is only 110 mVand the much broader IVCT transition is characteristic of a class II mixed-valence state. This is consistent with the observation that raising and lowering the energy of the d(π) orbitals in CH2Cl2 or water, respectively, will decrease or increase the energy gap to the LUMO of the bppz bridging ligand, which provides the delocalisation pathway via electron-transfer. IR spectroelectrochemistry could only be carried out successfully in CH2Cl2 and revealed class III mixed-valence behaviour on the fast IR timescale. In contrast to this, time-resolved IR spectroscopy showed that the MLCTexcited state, which is formulated as RuIII(bppz˙−)RuII and can therefore be considered as a mixed-valence Ru(II)/Ru(III) complex with an intermediate bridging radical anion ligand, is localised on the IR timescale with spectroscopically distinct Ru(II) and Ru(III) termini. This is because the necessary electron-transfer via the bppz ligand is more difficult because of the additional electron on bppz˙− which raises the orbital through which electron exchange occurs in energy. DFT calculations reproduce the electronic spectra of the complex in all three Ru(II)/Ru(II), Ru(II)/Ru(III) and Ru(III)/Ru(III) calculations in both water and CH2Cl2 well as long as an explicit allowance is made for the presence of water molecules hydrogen-bonded to the cyanides in the model used. They also reproduce the excited-state IR spectra of both [Ru(CN)4(μ-bppz)]2– and [{Ru(CN)4}2(μ-bppz)]4− very well in both solvents. The reorganization of the water solvent shell indicates a possible dynamical reason for the longer life time of the triplet state in water compared to CH2Cl2.