Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites

DNA-bending flexibility is central for its many biological functions. A new bending restraining method for use in molecular mechanics calculations and molecular dynamics simulations was developed. It is based on an average screw rotation axis definition for DNA segments and allows inducing continuous and smooth bending deformations of a DNA oligonucleotide. In addition to controlling the magnitude of induced bending it is also possible to control the bending direction so that the calculation of a complete (2-dimensional) directional DNA-bending map is now possible. The method was applied to several DNA oligonucleotides including A(adenine)-tract containing sequences known to form stable bent structures and to DNA containing mismatches or an abasic site. In case of G:A and C:C mismatches a greater variety of conformations bent in various directions compared to regular B-DNA was found. For comparison, a molecular dynamics implementation of the approach was also applied to calculate the free energy change associated with bending of A-tract containing DNA, including deformations significantly beyond the optimal curvature. Good agreement with available experimental data was obtained offering an atomic level explanation for stable bending of A-tract containing DNA molecules. The DNA-bending persistence length estimated from the explicit solvent simulations is also in good agreement with experiment whereas the adiabatic mapping calculations with a GB solvent model predict a bending rigidity roughly two times larger.     

Biphenylsulfonyl-thiophene-carboxamidine inhibitors of the complement component C1s

Complement activation has been implicated in disease states such as hereditary angioedema, ischemia-reperfusion injury, acute respiratory distress syndrome, and acute transplant rejection. Even though the complement cascade provides several protein targets for potential therapeutic intervention only two complement inhibitors have been approved so far for clinical use including anti-C5 antibodies for the treatment of paroxysmal nocturnal hemoglobinuria and purified C1-esterase inhibitor replacement therapy for the control of hereditary angioedema flares. In the present study, optimization of potency and physicochemical properties of a series of thiophene amidine-based C1s inhibitors with potential utility as intravenous agents for the inhibition of the classical pathway of complement is described.     

Surgical stabilisation of the spine compared with a programme of intensive rehabilitation for the management of patients with chronic low back pain: cost utility analysis based on a randomised controlled trial

Objective To determine whether, from a health provider and patient perspective, surgical stabilisation of the spine is cost effective when compared with an intensive programme of rehabilitation in patients with chronic low back pain.Design Economic evaluation alongside a pragmatic randomised controlled trial.Setting Secondary care.Participants 349 patients randomised to surgery (n = 176) or to an intensive rehabilitation programme (n = 173) from 15 centres across the United Kingdom between June 1996 and February 2002.Main outcome measures Costs related to back pain and incurred by the NHS and patients up to 24 months after randomisation. Return to paid employment and total hours worked. Patient utility as estimated by using the EuroQol EQ-5D questionnaire at several time points and used to calculate quality adjusted life years (QALYs). Cost effectiveness was expressed as an incremental cost per QALY.Results At two years, 38 patients randomised to rehabilitation had received rehabilitation and surgery whereas just seven surgery patients had received both treatments. The mean total cost per patient was estimated to be £7830 (SD £5202) in the surgery group and £4526 (SD £4155) in the intensive rehabilitation arm, a significant difference of £3304 (95% confidence interval £2317 to £4291). Mean QALYs over the trial period were 1.004 (SD 0.405) in the surgery group and 0.936 (SD 0.431) in the intensive rehabilitation group, giving a non-significant difference of 0.068 (–0.020 to 0.156). The incremental cost effectiveness ratio was estimated to be £48 588 per QALY gained (–£279 883 to £372 406).Conclusion Two year follow-up data show that surgical stabilisation of the spine may not be a cost effective use of scarce healthcare resources. However, sensitivity analyses show that this could change—for example, if the proportion of rehabilitation patients requiring subsequent surgery continues to increase.     

UV effects that come and go: a global comparison of marine benthic community level impacts

Ambient UV radiation has substantially increased during the last decades, but its impact on marine benthic communities is hardly known. The aim of this study was to globally compare and quantify how shallow hard‐bottom communities are affected by UV during early succession. Identical field experiments in 10 different coastal regions of both hemispheres produced a consistent but unexpected pattern: (i) UV radiation affected species diversity and community biomass in a very similar manner, (ii) diversity and biomass were reduced to a larger extent by UVA than UVB radiation, (iii) ambient UV levels did not affect the composition of the communities, and (iv) any UV effects disappeared during species succession after 2–3 months. Thus, current levels of UV radiation seem to have small, predictable, and transient effects on shallow marine hard‐bottom communities.     

Contrasting patterns of mussel abundance at neighbouring sites: does recruitment limitation explain the absence of mussels on Cook Strait (New Zealand) shores?

Wellington Harbour (New Zealand) supports large populations of mussels (Aulacomya maoriana, Mytilus galloprovincialis and Perna canaliculus), whereas these species are absent from Cook Strait shores only a few km away. The density of planktonic mussel larvae and their recruitment rates to artificial substrates were investigated at harbour (with mussels) and Cook Strait (no mussels) sites to determine if a diminished or a zero larval supply and/or settlement explains the absence of mussels from Cook Strait shores. At both locations, larvae were collected from the plankton approximately monthly between September 1998 and February 2000, and recruitment rates to artificial substrates were estimated between March 2000 and February 2001. Planktonic larval densities were almost an order of magnitude greater within the harbour than at coastal sites (mean (±S.D.) density was 982 m⁻³ (±1478) with a peak density in September 1998 of 4207 m⁻³, compared with 106 (±94) and 381 m⁻³, respectively, in March 1999). Larval recruitment at harbour sites was also significantly greater than at coastal sites (mean (±S.D.) recruitment density was 2169 m⁻² (±4207) with a peak of ca. 211,425 m⁻² in July 2000, compared with 88 m⁻² (±86) and ca. 3700 m⁻², respectively, in February 2001). It has been suggested that “bottom up” regulation of community structure, principally via a diet of particulates low in organic matter, is the explanation for the absence of suspension feeding mussels from Cook Strait sites [Helson, J. G., 2001. An investigation into the absence of mussels (Perna canalicus, Aulacomya maoriana and Mytilus galloprovincialis) from the South Coast of Wellington, New Zealand. Unpublished PhD thesis, Victoria University of Wellington, 183 pp.], but given that planktonic larval supply and recruitment rates are much reduced at coastal sites, these data may also be important in explaining the absence. Whether current levels of recruitment are sufficient to maintain an adult population is at present unknown and requires further examination.     

Residues in an ATP binding domain influence sugar binding in a trypanosome hexokinase

Trypanosoma brucei harbors two hexokinases (TbHK1 and TbHK2) that are 98% identical at the amino acid level. We previously found that recombinant TbHK1 (rTbHK1) has hexokinase activity, while rTbHK2 has not, a finding attributed to differences in the C-termini of the proteins. Sequence analysis suggests that the C-termini of TbHKs are part of a newly identified conserved motif found in other eukaryotic hexokinases. Here, we have explored the role of tail residues in the differences in catalytic activity between TbHK1 and TbHK2. Our studies reveal that tail residues D454, F462, M466, and N469 are essential for HK activity while both I458 and V468 are required for catalysis and substrate specificity. To activate rTbHK2, all of the residues important for activity in rTbHK1 (D454, V458, F462, M466, V468, and N469) were required. These results indicate that the overall structure of the C-terminal tail influences the HK activity of rTbHK1.     

Carbon isotope effect study on orotidine 5'-monophosphate decarboxylase: support for an anionic intermediate

Orotidine 5'-monophosphate decarboxylase has been heavily examined in recent years due to its enzymatic proficiency, which provides a catalytic enhancement to a reaction rate approximately 1017 times greater than that of the nonenzymatic reaction. Several mechanisms proposed to explain this catalytic enhancement have included covalent addition, ylide or carbene formation, and most recently concerted protonation. All of these mechanisms have circumvented the formation of a high-energy vinyl anionic intermediate. To investigate the presence of an anionic intermediate, 13C isotope effect studies have been performed using the alternate substrate 5-fluoro-OMP (OMP = orotidine 5'-monophosphate). Isotope effects obtained for the wild-type enzyme with OMP and 5-fluoro-OMP are 1.0255 and 1.0106, respectively, corresponding to a decrease of approximately 1.5% for 5-fluoro-OMP. With the K59A enzyme, the intrinisic isotope effects show a similar decrease of approximately 1.9% from 1.0543 with OMP to 1.0356 with 5-fluoro-OMP. This decrease results from the inductive effect of the fluorine, which stabilizes the carbanion intermediate by electron withdrawal and produces a reaction with an earlier transition state. The isotope effect for the decarboxylation of the slow substrate 2'-deoxy-OMP produced a intrinsic isotope effect of nearly 1.0461.