Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA

Mechanistic models of charge transfer (CT) in macromolecules often focus on CT energetics and distance as the chief parameters governing CT rates and efficiencies. However, in DNA, features unique to the DNA molecule, in particular, the structure and dynamics of the DNA base stack, also have a dramatic impact on CT. Here we probe the influence of subtle structural variations on base-base CT within a DNA duplex by examining photoinduced quenching of 2-aminopurine (Ap) as a result of hole transfer (HT) to guanine (G). Photoexcited Ap is used as a dual reporter of variations in base stacking and CT efficiency. Significantly, the unique features of DNA, including the strandedness and directional asymmetry of the double helix, play a defining role in CT efficiency. For an (AT)(n) bridge, the orientation of the base pairs is critical; the yield of intrastrand HT is markedly higher through (A)n compared with (T)(n) bridges, whereas HT via intrastrand pathways is more efficient than through interstrand pathways. Remarkably, for reactions through the same DNA bridge, over the same distance, and with the same driving force, HT from photoexcited Ap to G in the 5' to 3' direction is more efficient and less dependent on distance than HT from 3' to 5'. We attribute these differences in HT efficiency to variations in base-base coupling within the DNA assemblies. Thus base-base coupling is a critical parameter in DNA CT and strongly depends on subtle structural nuances of duplex DNA

Superorbital Period in the High Mass X-ray Binary 2S 0114+650

We report the detection of a superorbital period in the high-mass X-ray binary 2S 0114+650. Analyses of data from the Rossi X-ray Timing Explorer (RXTE) All-Sky Monitor (ASM) from 1996 January 5 to 2004 August 25 reveal a superorbital period of 30.7 +/- 0.1 d, in addition to confirming the previously reported neutron star spin period of 2.7 h and the binary orbital period of 11.6 d. It is unclear if the superorbital period can be ascribed to the precession of a warped accretion disc in the system.Comment: 5 pages, 5 figures, submitted to MNRAS 27th January 2005. Manuscript expanded to include discussion of evolution of periods, and hardness ratio variability. Number of figures increased from 5 to 9. Accepted for publication 19th December 200

Copasetic analysis: Automated analysis of biological gene expression images

Copyright [2004] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.In the past decade computational biology has come to the forefront of the public's perception with advancements in domain knowledge and a variety of analysis techniques. With the recent completion of projects like the human genome sequence, and the development of microarray chips it has become possible to simultaneously analyse expression levels for thousands of genes. Typically, a slide surface of less than 24 cm2, receptors for 30,000 genes can be printed, but currently the analysis process is a time consuming semi-autonomous step requiring human guidance. The paper proposes a framework, which facilitates automated processing of these images. This is supported by real world examples, which demonstrate the technique's capabilities along with results, which show a marked improvement over existing implementations

A Multicoloured View of 2S 0114+650

We report the results of radio and X-ray observations of the high mass X-ray binary 2S 0114+650, made with the Giant Meterwave Radio Telescope and the Rossi X-ray Timing Explorer respectively. No emission was detected at radio wavelengths. The neutral hydrogen column density was found to vary over the orbital period, while no variability over the the super-orbital period was observed. We discuss the causes of the observed relationships and the implications for the underlying mechanisms.Comment: 4 pages, 2 figures; to appear in proceedings for "The multicoloured landscape of compact objects and their explosive progenitors", Cefalu, Sicily, 2006 June 11-24, AIP, submitte

In-Chain Tunneling Through Charge-Density Wave Nanoconstrictions and Break-Junctions

We have fabricated longitudinal nanoconstrictions in the charge-density wave conductor (CDW) NbSe$_{3}$ using a focused ion beam and using a mechanically controlled break-junction technique. Conductance peaks are observed below the T$_{P1}$$=145$K and T$_{P2}$$=59$K CDW transitions, which correspond closely with previous values of the full CDW gaps $2\Delta_{1}$ and $2\Delta_{2}$ obtained from photo-emission. These results can be explained by assuming CDW-CDW tunneling in the presence of an energy gap corrugation $\epsilon_{2}$ comparable to $\Delta_{2}$, which eliminates expected peak at $\Delta_{1}+\Delta_{2}$. The nanometer length-scales our experiments imply indicate that an alternative explanation based on tunneling through back-to-back CDW-normal junctions is unlikely.Comment: 5 pages, 3 figures, submitted to physical review letter

Recurrent ~24 h Periods in RXTE ASM Data

Analysis of data from the Rossi X-ray Timing Explorer satellite's All Sky Monitor instrument for several X-ray binary sources has identified a recurrent \~24 h period. This period is sometimes highly significant, giving rise to the possibility of it being identified as an orbital or super-orbital period. Further analysis has revealed the same period in a number of other X-ray sources. As a result this period has been discounted as spurious, described variously as arising from daily variations in background levels and beating between the sampling period and long-term secular trends in the light curves. We present here an analysis of the spurious periods and show that the dominant mechanism is in fact spectral leakage of low-frequency power present in the light curves.Comment: 9 Pages, 10 figures, 1 table, submitted to PASA 20th December 2004. Added 1 page of text and 3 figures to clarify results and discussion. Resubmitted 16th May 2005. Accepted 25th June 200