Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase.

DNA strand exchange by serine recombinases has been proposed to occur by a large-scale rotation of halves of the recombinase tetramer. Here we provide the first direct physical evidence for the subunit rotation mechanism for the Hin serine invertase. Single-DNA looping assays using an activated mutant (Hin-H107Y) reveal specific synapses between two hix sites. Two-DNA "braiding" experiments, where separate DNA molecules carrying a single hix are interwound, show that Hin-H107Y cleaves both hix sites and mediates multi-step rotational relaxation of the interwinding. The variable numbers of rotations in the DNA braid experiments are in accord with data from bulk experiments that follow DNA topological changes accompanying recombination by the hyperactive enzyme. The relatively slow Hin rotation rates, combined with pauses, indicate considerable rotary friction between synapsed subunit pairs. A rotational pausing mechanism intrinsic to serine recombinases is likely to be crucial for DNA ligation and for preventing deleterious DNA rearrangements

Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion.

Serine recombinases are often tightly controlled by elaborate, topologically-defined, nucleoprotein complexes. Hin is a member of the DNA invertase subclass of serine recombinases that are regulated by a remote recombinational enhancer element containing two binding sites for the protein Fis. Two Hin dimers bound to specific recombination sites associate with the Fis-bound enhancer by DNA looping where they are remodeled into a synaptic tetramer competent for DNA chemistry and exchange. Here we show that the flexible beta-hairpin arms of the Fis dimers contact the DNA binding domain of one subunit of each Hin dimer. These contacts sandwich the Hin dimers to promote remodeling into the tetramer. A basic region on the Hin catalytic domain then contacts enhancer DNA to complete assembly of the active Hin tetramer. Our results reveal how the enhancer generates the recombination complex that specifies DNA inversion and regulates DNA exchange by the subunit rotation mechanism. DOI:http://dx.doi.org/10.7554/eLife.01211.001

Turbomachinery

The discipline research in turbomachinery, which is directed toward building the tools needed to understand such a complex flow phenomenon, is based on the fact that flow in turbomachinery is fundamentally unsteady or time dependent. Success in building a reliable inventory of analytic and experimental tools will depend on how the time and time-averages are treated, as well as on who the space and space-averages are treated. The raw tools at disposal (both experimentally and computational) are truly powerful and their numbers are growing at a staggering pace. As a result of this power, a case can be made that a situation exists where information is outstripping understanding. The challenge is to develop a set of computational and experimental tools which genuinely increase understanding of the fluid flow and heat transfer in a turbomachine. Viewgraphs outline a philosophy based on working on a stairstep hierarchy of mathematical and experimental complexity to build a system of tools, which enable one to aggressively design the turbomachinery of the next century. Examples of the types of computational and experimental tools under current development at Lewis, with progress to date, are examined. The examples include work in both the time-resolved and time-averaged domains. Finally, an attempt is made to identify the proper place for Lewis in this continuum of research

Case history and persistence of the non-indigenous diatom Coscinodiscus wailesii in the north-east Atlantic

The introduction of non-indigenous marine plankton species can have a considerable ecological and economic effect on regional systems. Their presence, however, can go unnoticed until they reach nuisance status and as a consequence few case histories exist containing information on their initial appearance and their spatio-temporal patterns. Here we report on the occurrence of the non-indigenous diatom Coscinodiscus wailesii in 1977 in the English Channel, its subsequent geographical spread into European shelf seas, and its persistence as a significant member of the diatom community in the north-east Atlantic from 1977-1995

Turbomachinery

The discipline research in turbomachinery, which is directed toward building the tools needed to understand such a complex flow phenomenon, is based on the fact that flow in turbomachinery is fundamentally unsteady or time dependent. Success in building a reliable inventory of analytic and experimental tools will depend on how we treat time and time-averages, as well as how we treat space and space-averages. The challenge is to develop a set of computational and experimental tools which genuinely increase our understanding of the fluid flow and heat transfer in a turbomachine. Examples of the types of computational and experimental tools under current development, with progress to date, are examined. The examples include work in both the time-resolved and time-averaged domains

Pulse source for 80 Gb/s systems using a gain-wwitched laser diode followed by a nonlinearly chirped grating

This work presents the generation of 3.5 ps pulses at a repetition rate of 10 GHz and the optimization of the pulse spectrum. The output pulses are near transform limited and have pulse pedestals that are virtually eliminated to 35 dB down from the peak of the pulse, thus providing a source suitable for use in 80 Gb/s OTDM systems

Optimized pulse source employing an externally injected gain-switched laser diode in conjunction with a nonlinearly chirped grating

In this paper, we demonstrate the generation of transform-limited short optical pulses, which display excellent spectral and temporal qualities by employing a novel technology, based on an externally injected gain-switched laser in conjunction with a nonlinearly chirped grating. Using this technique, 3.5-ps optical pulses exhibiting a time-bandwidth product (TBP) of 0.45 are generated, which are suitable for use in high-speed 80 Gb/s optical time-division multiplexing (OTDM) communications systems. The numerical integration of a set of rate equations using suitable parameters for the devices used in the experiments were carried out to further confirm the feasibility of the proposed method for developing an optimized pulse source for high-speed photonic systems

Analysis of bit rate dependence up to 80 Gbit/s of a simple wavelength converter based on XPM in a SOA and a shifted filtering

This paper provides the analysis of wavelength converted pulses obtained with a simple semiconductor optical amplifier (SOA)-based wavelength conversion scheme, which exploits cross phase modulation (XPM) in an SOA in conjunction with shifted filtering. The analysis includes experimental measurements of the back-to-back system performances as well as frequency-resolved optical gating (FROG) characterisations of the wavelength converted pulses. These measurements are implemented at different bit rates up to 80 Gbit/s and for both red and blue-shifted filtering, particularly showing different patterning effect dependencies of red and blue-shifting techniques. This analysis is developed by the addition of a numerical study which corroborates the experimental results. A further understanding of the different performances of red and blue filtering techniques, presented in the literature, can thus be proposed. The placement of the filter to undertake red-shifted filtering (RSF) allows us to achieve very short pulse widths but high bit rate operation is limited by pattern effects. The blue-shifted filtering (BSF) technique shows optimum performance as regards to patterning effects even if the wavelength converted pulses can be larger

Anomalous near-field heat transfer between a cylinder and a perforated surface

We predict that the radiative heat-transfer rate between a cylinder and a perforated surface depends non-monotonically on their separation. This anomalous behavior, which arises due to near-field effects, is explained using a heuristic model based on the interaction of a dipole with a plate. We show that nonmonotonicity depends not only on geometry and temperature but also on material dispersion - for micron and submicron objects, nonmonotonicity is present in polar dielectrics but absent in metals with small skin depths