Temperature dependence of Raman vibrational bandwidths in poly(rA) and rAMP

Isotropic and anisotropic spontaneous Raman spectra were obtained from solutions of poly(ra) and rAMP in buffer. The temperature dependence of these spectra was measured to elucidate the influence of macromolecular dynamics and solvent dynamics on the bandwidths of base vibrations in the single stranded polynucleotide poly(rA). The temperature dependence of a bandwidth depends upon the particular vibration under study. The bands can for the larger part be described by Lorentz functions. When fitted by Voigt functions, maximally 10% of each bandprofile of the adenine base vibrations can be attributed to a Gaussian component. The second moment has been determined from the spectra for the 725 cm¿1 band. From the second moment and the bandwidth, we were able to deduce that the vibrational oscillator is in the fast modulation limit. The determined timescale (perturbation correlation time 0.13 ps) eliminate perturbations connected to long range diffusion like concentration fluctuations (timescale in the order of 10 ps). The spectra were analyzed by an extensive curve fitting procedure providing accurate bandparameters (position, width and integrated intensity). The 725 cm¿1 band of adenine has a bandwidth which is dependent upon the degree of polymerization. In RAMP it is 17.6 cm¿1, in stacked (i.e. low temperature 5°C) poly(rA) it is 11.5 cm¿1. The bandwidth of the adenine vibration at 1336 cm¿1 cm¿1 has a temperature dependence which is similar to the intensity changes of the Raman and the absorption hypochromic effect as a function of temperature. The melting transition can therefore be followed by the changes in bandwidth of suitable vibrations

A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4

Raman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co-workers [M. Berjot, L. Marx, and A.J.P. Alix (1985) J. Ramanspectrosc., submitted; A.J.P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149-154], 1 gp32 contains ≈ 45% helix, ≈ 40% β-sheet, and 15% undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4-6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO- groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide-protein complexes the nucleotide shields the 4-6 tyrosine residues from coordination by the COO- groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single-stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more -sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate-sugar-base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm-1 in poly(rA), at 1230 cm-1 in poly(rU), and at 1240 and 1378 cm-1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8

Hydrographs by Single Linear Reservoir Model

A single linear reservoir (SLR) model is presented which provides a simple means for developing runoff hydrographs for small, urban watersheds. The model only requires one parameter, K, which can be estimated from watershed and precipitation characteristics. Several methods for estimating K and the results of testing the model on various watersheds are presented.Waller Creek Working Grou

The Resonance Overlap and Hill Stability Criteria Revisited

We review the orbital stability of the planar circular restricted three-body problem, in the case of massless particles initially located between both massive bodies. We present new estimates of the resonance overlap criterion and the Hill stability limit, and compare their predictions with detailed dynamical maps constructed with N-body simulations. We show that the boundary between (Hill) stable and unstable orbits is not smooth but characterized by a rich structure generated by the superposition of different mean-motion resonances which does not allow for a simple global expression for stability. We propose that, for a given perturbing mass $m_1$ and initial eccentricity $e$, there are actually two critical values of the semimajor axis. All values $a a_{\rm unstable}$ are unstable in the Hill sense. The first limit is given by the Hill-stability criterion and is a function of the eccentricity. The second limit is virtually insensitive to the initial eccentricity, and closely resembles a new resonance overlap condition (for circular orbits) developed in terms of the intersection between first and second-order mean-motion resonances.Comment: 33 pages, 14 figures, accepte

MAMA: An Algebraic Map for the Secular Dynamics of Planetesimals in Tight Binary Systems

We present an algebraic map (MAMA) for the dynamical and collisional evolution of a planetesimal swarm orbiting the main star of a tight binary system (TBS). The orbital evolution of each planetesimal is dictated by the secular perturbations of the secondary star and gas drag due to interactions with a protoplanetary disk. The gas disk is assumed eccentric with a constant precession rate. Gravitational interactions between the planetesimals are ignored. All bodies are assumed coplanar. A comparison with full N-body simulations shows that the map is of the order of 100 times faster, while preserving all the main characteristics of the full system. In a second part of the work, we apply MAMA to the \gamma-Cephei, searching for friendly scenarios that may explain the formation of the giant planet detected in this system. For low-mass protoplanetary disks, we find that a low-eccentricity static disk aligned with the binary yields impact velocities between planetesimals below the disruption threshold. All other scenarios appear hostile to planetary formation

The MCGA (multiple cubic gradient approximation) method for the analysis of Raman spectra

An easily accessible interactive method for the analysis of Raman spectra consisting of many overlapping peaks is presented. A combination of a three- or four-dimensional grid and gradient searching is applied. The method can handle spectra with up to about 50 lines, based on a broad background. Analytical and user-defined or tabulated basic functions can be included. The merits of the method are discussed with both artificial and real spectra

Surface-enhanced Raman spectroscopy of DNA bases

A Raman microprobe has been used to measure the surface-enhanced Raman spectra of adenine, guanine, cytosine and thymine. Comparison of the SERS spectrum with solution spectra shows that some line positions are not influenced by the adsorption process while others show large shifts. In the SERS spectrum new lines, not visible in the solution spectrum, appear while some lines visible in the solution spectrum are not enhanced to a detectable level and are therefore not seen in SERS. The relative intensities are changed owing to an apparently vibration-dependent enhancement factor. A line-broadening effect occurs for most lines except carbonyl stretching vibrations in cytosine and thymine. All SERS spectra show increased contributions of bending vibrations and side-chain groups. In particular, amino group vibrations in adenine and cytosine are clearly visible. Comparison of the shape and intensity of the carbonyl stretching vibrations in cytosine, thymine and guanine show important differences. It is hypothesized that these differences indicate differences in the orientation of these groups with respect to the surface

Development of an Integrated Governance Strategy for the Voluntary and Community Sector

This report on governance provides a framework for thinking about how policy makers, funders,regulators and advisers can all work with Board members and staff to enhance the effectiveness of nonprofit organisations. It was commissioned by the Active Community Unit (ACU) of the Home Office, in parallel with other reviews designed to improve the capacity of the voluntary and community sector, at a time when the sector plays an increasingly important role in the delivery of services using public funds. That role has recently been investigated in two Government reports, the Cross Cutting Review carried out by the Treasury, and the Strategy Unit review of charities and nonprofits. Our report proposes actions of three types: some that can be taken immediately, some that require further discussion with key interests, and some integration with the other ACU reviews. Taken together they provide the starting point for an evolving strategy to improve governance across the sector. We recommend ACU chairs a group charged with the responsibility for planning and implementing this. Our focus is on governance as 'the systems and processes concerned with ensuring the overall direction, supervision and accountability of an organisation'. This is often taken to mean the way that a Board, management committee or other governing body steers the overall development of an organisation, where day-to-day management is in the hands of staff or volunteers. Sometimes, of course, the committee and volunteers are the same. They – like all governing bodies – have to balance the interests of the organisation and those they are trying to serve, while being conscious of financial and legal responsibilities, and the requirements of funders and other supporters