Translating colorectal cancer genetics into clinically useful biomarkers.

Colorectal cancer (CRC) is a major health problem worldwide accounting for over a million deaths annually. While many patients with Stage II and III CRC can be cured with combinations of surgery, radiotherapy and chemotherapy, this is morbid costly treatment and a significant proportion will suffer recurrence and eventually die of CRC. Increased understanding of the molecular pathogenesis of CRC has the potential to identify high risk patients and target therapy more appropriately. Despite increased understanding of the molecular events underlying CRC development, established molecular techniques have only produced a limited number of biomarkers suitable for use in routine clinical practice to predict risk, prognosis and response to treatment. Recent rapid technological developments, however, have made genomic sequencing of CRC more economical and efficient, creating potential for the discovery of genetic biomarkers that have greater diagnostic, prognostic and therapeutic capabilities for the management of CRC. This paper reviews the current understanding of the molecular pathogenesis of CRC, and summarizes molecular biomarkers that surgeons will encounter in current clinical use as well as those under development in clinical and preclinical trials. New molecular technologies are reviewed together with their potential impact on the understanding of the molecular pathogenesis of CRC and their potential clinical utility in classification, diagnosis, prognosis and targeting of therapy.

Impaired Coronary Endothelial Vasorelaxation in a Preclinical Model of Peripheral Arterial Insufficiency.

The present study was designed to determine whether adult swine with peripheral artery insufficiency (PAI) would exhibit vascular dysfunction in vessels distinct from the affected distal limbs, the coronary conduit arteries. Moreover, we sought to evaluate the effect of exercise training on coronary vasomotor function in PAI. Eighteen female healthy young Yucatan miniature swine were randomly assigned to either occluded exercise trained (Occl-Ex, n=7), or occluded-sedentary (Occl-Sed, n=5), or non-occluded, non-exercised control (Non-Occl-Con, n=6) groups. Occl-Ex pigs were progressively trained by running on a treadmill (5days/week, 12 weeks). The left descending artery (LAD) and left circumflex (LCX) coronary arteries were harvested. Vasorelaxation to adenosine diphosphate (ADP), bradykinin (BK), and sodium nitro-prusside (SNP) were assessed in LAD's; while constrictor responses to phenylephrine (PE), angiotensin II (Ang II), and endothelin-1 (ET-1) were assessed in LCX's. Vasorelaxation to ADP was reduced in LADs from Occl-Sed and Occl-Ex pigs (P<0.001) as compared to Non-Occl-Con pigs; however, Occl-Ex pigs exhibited partial recovery (P<0.001) intermediate to the other two groups. BK induced relaxation was reduced in LADs from Occl-Ex and Occl-Sed pigs (P<0.001), compared to Non-Occl-Con, and exercise modestly increased responses to BK (P<0.05). In addition, SNP, PE, Ang II, and ET-1 responses were not significantly different among the groups. Our results indicate that 'simple' occlusion of the femoral arteries induces vascular dysfunction in conduit vessels distinct from the affected hindlimbs, as evident in blunted coronary vasorelaxation responses to ADP and BK. These findings imply that PAI, even in the absence of frank atherogenic vascular disease, contributes to vascular dysfunction in the coronary arteries that could exacerbate disease outcome in patients with peripheral artery disease. Further, regular daily physical activity partially recovered the deficit observed in the coronary arteries.

Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity.

We used the crystal structure of prolyl oligopeptidase (POP) with bound Z-pro-prolinal (ZPP) inhibitor (Protein Data Bank (PDB) structure 1QFS) to perform an intensive molecular dynamics study of the POP-ZPP complex. We performed 100 ns of simulation with the hemiacetal bond, through which the ZPP is bound to the POP, removed in order to better investigate the binding cavity environment. From basic analysis, measuring the radius of gyration, root mean square deviation, solvent accessible surface area and definition of the secondary structure of protein, we determined that the protein structure is highly stable and maintains its structure over the entire simulation time. This demonstrates that such long time simulations can be performed without the protein structure losing stability. We found that water bridges and hydrogen bonds play a negligible role in binding the ZPP thus indicating the importance of the hemiacetal bond. The two domains of the protein are bound by a set of approximately 12 hydrogen bonds, specific to the particular POP protein.

HSE's Safety Assessment Principles for radiation protection.

The Health and Safety Executive (HSE) published its revised Safety Assessment Principles for Nuclear Facilities (SAPs) in December 2006. The SAPs are primarily intended for use by HSE's inspectors when judging the adequacy of safety cases for nuclear facilities. The revised SAPs refer in part to HSE's expectations relating to the technical discipline of radiation protection. The purpose of this paper is to describe for the benefit of a wider audience HSE's reasoning behind the final published SAPs and to set out the purpose of each specific radiation protection (RP) principle. The paper also discusses principles in other sections of the SAPs which are relevant to radiation protection. The paper notes that the SAPs should be viewed as a reflection of good practice in relation to nuclear facilities in the context of interpreting relevant parts of primary legislation such as the Nuclear Installations Act 1965.

Molecular dynamics simulations of the enzyme catechol-O-methyltransferase: methodological issues.

Results from extensive 70 ns all-atom molecular dynamics simulations of catechol-O-methyltransferase (COMT) enzyme are reported. The simulations were performed with explicit TIP3P water and Mg2+ ions. Four different crystal structures of COMT, with and without different ligands, were used. These simulations are among the most extensive of their kind and as such served as a stability test for such simulations. On the methodological side we found that the initial energy minimization procedure may be a crucial step: particular hydrogen bonds may break, and this can initiate an irreversible loss of protein structure that becomes observable in longer time scales of the order of tens of nanoseconds. This has important implications for both molecular dynamics and quantum mechanics-molecular mechanics simulations.

Ultra-relativistic electrons in Jupiter's radiation belts.

Ground-based observations have shown that Jupiter is a two-component source of microwave radio emission: thermal atmospheric emission and synchrotron emission from energetic electrons spiralling in Jupiter's magnetic field. Later in situ measurements confirmed the existence of Jupiter's high-energy electron-radiation belts, with evidence for electrons at energies up to 20[?]MeV. Although most radiation belt models predict electrons at higher energies, adiabatic diffusion theory can account only for energies up to around 20[?]MeV. Unambiguous evidence for more energetic electrons is lacking. Here we report observations of 13.8[?]GHz synchrotron emission that confirm the presence of electrons with energies up to 50[?]MeV; the data were collected during the Cassini fly-by of Jupiter. These energetic electrons may be repeatedly accelerated through an interaction with plasma waves, which can transfer energy into the electrons. Preliminary comparison of our data with model results suggests that electrons with energies of less than 20[?]MeV are more numerous than previously believed.

Parallel excluded volume tempering for polymer melts.

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts that makes use of both parallel tempering and large-scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large-scale Monte Carlo moves through attempted pivot and translation moves that reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as N=60 monomers, however at this chain length the large-scale Monte Carlo moves were ineffective. For even longer chains, the speedup becomes substantial, as observed from preliminary data for N=200. We also compare our scheme to the end bridging algorithm of Theodorou et al. For N=60, end bridging must allow a polydispersity of more than 10% in order to relax the end-to-end vector more quickly than our method. The comparison is, however, hampered by the fact that the end-to-end vector becomes a somewhat artificial quantity when one implements end bridging, and is perhaps no longer the slowest dynamic variable.

Rational design, synthesis, and biological activity of benzoxazinones as novel factor Xa inhibitors.

Inappropriate thrombus formation within blood vessels is the leading cause of mortality in the industrialized world. Factor Xa (FXa) is a trypsin-like serine protease that plays a key role in the blood coagulation cascade and represents an attractive target for anticoagulant drug development. From a high-throughput in vitro mass screen of our chemical library, we identified 4-[5-[(2R,6S)-2, 6-dimethyltetrahydro-1(2H)-pyridinyl]pentyl]-2-phenyl-2H-1, 4-benzoxazin-3(4H)-one (1a) as an inhibitor of FXa with an IC(50) of 27 microM. Through a combination of SAR studies and molecular modeling, we synthesized 3-(4-[5-[(2R,6S)-2, 6-dimethyltetrahydro-1(2H)-pyridinyl]pentyl]-3-oxo-3,4-dihydro-2H- 1,4-benzoxazin-2-yl)-1-benzenecarboximidamide (1n) which was a potent FXa inhibitor with an IC(50) of 3 nM. This compound exhibited high selectivity for FXa over other related serine proteases and was efficacious when dosed intravenously in rabbit and dog antithrombotic models.

Longitudinal magnetic excitations in classical spin systems

Using spin dynamics simulations we predict the splitting of the longitudinal spin-wave peak in all antiferromagnets with single site anisotropy into two peaks separated by twice the energy gap at the Brillouin zone center. This phenomenon has yet to be observed experimentally but can be easily investigated through neutron scattering experiments on MnF2 and FeF2. We have also determined that for all classical Heisenberg models the longitudinal propagative excitations are entirely multiple spin wave in nature.

Endothelin receptor antagonists: synthesis and structure-activity relationships of substituted benzothiazine-1,1-dioxides.

The development of benzothiazine-1,1-dioxide derivatives as a new structural class of potent endothelin receptor antagonists is described. Structure-activity relationships (SAR) revealed that PD164800 (1) is a potent antagonist of the ETA receptor subtype.

A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1.

BACKGROUND: Channel-forming colicins, including colicin E1, are a sub-family of bacteriocins. The toxic action of colicin E1 is derived from its ability to form a voltage-gated channel, which causes depolarization of the cytoplasmic membrane of sensitive Escherichia coli cells. In this process, the toxin-like colicin E1 molecule must undergo a substantial structural transition from a soluble state, in which it binds the target cell, to a membrane-bound state. Details of the structural changes that accompany this conversion may be directly applicable to other channel-forming toxins, as well as to the mechanism by which proteins insert into or cross membranes. RESULTS: The structure of the 190-residue channel-forming domain of colicin E1 in its soluble form has been solved at 2.5 A resolution. This structure contains 10alpha helices arranged in three layers (A-C) with a central hydrophobic helical hairpin in layer B, which is proposed to anchor the membrane-bound form in the bilayer. The extended N-terminal helix I provides a connection to the rest of the colicin E1 molecule, and the loop I-II may act as a hinge for re-orientation of the domain for membrane binding. A set of conserved positively charged residues on layer C may provide the docking surface on the molecule for membrane attachment. A large internal cavity between layers B and C may allow these layers to disengage, suggesting a mechanism for unfolding the molecule on the membrane that involves the perturbation of the interhelical hydrophobic interactions in layer C. CONCLUSION: On the basis of the structure of the colicin E1 channel-forming domain, its comparison with the structure of the colicin A domain and the known requirement for initial electrostatic and subsequent hydrophobic interactions, molecular details of the docking, unfolding and insertion of the channel-forming domain into the membrane are proposed. The model for docking and initial interaction with the membrane positions the hydrophobic hairpin 'anchor' approximately parallel to the membrane surface. Hydrophobic interactions in the docking layer may then be displaced by interactions with the membrane, spreading the helices on the surface and exposing the hydrophobic hairpin for insertion into the membrane.

Derivatives of 5-[[1-(4'-carboxybenzyl)imidazolyl]methylidene]hydantoins as orally active angiotensin II receptor antagonists.

A series of 5-[[1-(4'-carboxybenzyl)imidazolyl]methylidene]hydantoins have been prepared and evaluated as in vitro and in vivo angiotensin II (Ang II) antagonists. Variation of substituents on the hydantoin ring leads to potent and selective Ang II antagonists with nanomolar IC50 values at the AT1 receptor and negligible affinity for the AT2 receptor. Preferred substituents include an n-butyl at R1 and an alkyl or heteroarylmethyl substituent at R2. The selection of the R2 substituent was guided in part by the calculation of its log P since a significant correlation was observed between CLOGP and AT1 binding affinity. The biphenyl tetrazole pharmacophore, common to a number of AT1 antagonists, could be replaced by, for example, a 4-carbomethoxyphenyl substituent resulting in potent Ang II antagonists both in vitro and in vivo. A representative compound of this series is 57, which reduced the mean arterial blood pressure of renal hypertensive rats by 40% at 30 mg/kg po and by 25% at 10 mg/kg po. In addition this compound was efficacious in the salt-deplete normotensive monkey model maximally decreasing blood pressure 27% at 10 mg/kg po. In summary, these compounds belong to a novel class of Ang II antagonists that lack the biphenyl tetrazole moiety yet display appreciable and long lasting oral activity.

Nonpeptide angiotensin II receptor antagonists. 2. Design, synthesis, and structure-activity relationships of 2-alkyl-4-(1H-pyrrol-1-yl)-1H-imidazole derivatives: profile of 2-propyl-1-[[2'-(1H-tetrazol-5-yl)-[1,1' -biphenyl]-4-yl]-methyl]-4-[2-(trifluoroacetyl)-1H-pyrrol-1-yl]-1H- imidazole-5-carboxylic acid (CI-996).

A novel series of nonpeptide angiotensin II (AII) receptor antagonists containing a 1H-pyrrol-1-yl moiety at the 4-position of the imidazole have been developed. The pyrrole group occupies the same lipophilic pocket at the receptor as the chloro group in DuP 753 (68) and EXP 3174 (69) and the pentafluoro group in DuP 532 (70), respectively. The impetus for its selection came from bioisosteric considerations based on hydrophobic and electronic substituent constants. An extensive study of the structure-activity relationships revealed several highly potent AII receptor antagonists. An acyl substitution at the 2-position of the pyrrole ring improved activity, most notably in the in vivo rat model. In addition, the 2-substituted pyrrole compounds improved chemical stability toward extremely facile decarboxylation reaction associated with unsubstituted pyrrole analogues, thus facilitating development of these agents. The IC50's of 18, 20, and 42 (< 1 nM) were better than the reference compounds 69 and 70, respectively. These compounds were selective AII antagonists that compete at the AT1 receptor and showed no affinity at the AT2 receptor at concentrations up to 10 microM. Upon intravenous administration in a normotensive rat model, compound 18 inhibited the AII-induced responses with ED50 of 6 micrograms/kg per min. In a renal hypertensive rat model, the antihypertensive potency of compound 18, at a dose of 10 mg/kg, was very similar to those 68 and 69, respectively. Compound 18 demonstrated a dose-related (3-30 mg/kg) decrease in blood pressure that was sustained for greater than 24 h. On the basis of its profile, compound 18, designated as CI-996, has been selected for in-depth studies. The design, synthesis, in vitro, and in vivo structure-activity relationships are described.

A new look at the saturn system: the voyager 2 images.

Voyager 2 photography has complemented that of Voyager I in revealing many additional characteristics of Saturn and its satellites and rings. Saturn's atmosphere contains persistent oval cloud features reminiscent of features on Jupiter. Smaller irregular features track out a pattern of zonal winds that is symmetric about Saturn's equator and appears to extend to great depth. Winds are predominantly eastward and reach 500 meters per second at the equator. Titan has several haze layers with significantly varying optical properties and a northern polar "collar" that is dark at short wavelengths. Several satellites have been photographed at substantially improved resolution. Enceladus' surface ranges from old, densely cratered terrain to relatively young, uncratered plains crossed by grooves and faults. Tethys has a crater 400 kilometers in diameter whose floor has domed to match Tethys' surface curvature and a deep trench that extends at least 270 degrees around Tethys' circumference. Hyperion is cratered and irregular in shape. Iapetus' bright, trailing hemisphere includes several dark-floored craters, and Phoebe has a very low albedo and rotates in the direction opposite to that of its orbital revolution with a period of 9 hours. Within Saturn's rings, the "birth" of a spoke has been observed, and surprising azimuthal and time variability is found in the ringlet structure of the outer B ring. These observations lead to speculations about Saturn's internal structure and about the collisional and thermal history of the rings and satellites.

Encounter with saturn: voyager 1 imaging science results.

As Voyager 1 flew through the Saturn system it returned photographs revealing many new and surprising characteristics of this complicated community of bodies. Saturn's atmosphere has numerous, low-contrast, discrete cloud features and a pattern of circulation significantly different from that of Jupiter. Titan is shrouded in a haze layer that varies in thickness and appearance. Among the icy satellites there is considerable variety in density, albedo, and surface morphology and substantial evidence for endogenic surface modification. Trends in density and crater characteristics are quite unlike those of the Galilean satellites. Small inner satellites, three of which were discovered in Voyager images, interact gravitationally with one another and with the ring particles in ways not observed elsewhere in the solar system. Saturn's broad A, B, and C rings contain hundreds of "ringlets," and in the densest portion of the B ring there are numerous nonaxisymmetric features. The narrow F ring has three components which, in at least one instance, are kinked and crisscrossed. Two rings are observed beyond the F ring, and material is seen between the C ring and the planet.