Features and development of Coot.

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

Food safety knowledge and practices in ready-to-eat food establishments.

Safe food handling in ready-to-eat food establishments is a basic element in the reduction of foodborne illness. The aim of this research was to investigate (using a questionnaire), knowledge and attitudes about food safety held by management and staff in ready-to-eat food establishments. Fieldwork was conducted in 2002 in Wellington City, New Zealand. Managers rated 'staff with good food safety knowledge' the most important aspect of ensuring safe food. Half of these managers were prepared to pay higher wages to staff holding a current food safety certificate. Although respondents considered that closure of the establishment was the most serious business consequence of a breakdown in safe food handling, less than half (49%) were prepared to pay an additional insurance premium to cover this risk. All food handling workers should be encouraged to obtain and maintain a current food safety certificate. Environmental health officers who inspect ready-to-eat food establishments play an important role in guiding and assisting owners and staff in improving food handling standards.

Ribozyme catalysis via orbital steering.

Orbital steering is invoked to explain how the three-dimensional structure of a small self-cleaving RNA, the hammerhead ribozyme, both prevents and enhances RNA autocatalysis. Within the conserved catalytic core of the ribozyme, the position of the 2' oxygen atom of the G8 ribose is observed to be aligned almost perfectly with the phosphorus atom and the 5' oxygen atom of the adjacent A9 phosphate group for self-cleavage via an in-line attack mechanism. Despite this apparent near-perfect atomic positioning, no cleavage takes place. The explanation proposed is that a network of hydrogen bonds in the ribozyme core orients or steers the orbitals containing the electron lone pairs of the attacking nucleophile (the 2' oxygen atom) away from the A9 phosphorus atom, eliminating overlap with the vacant phosphorus d-orbitals despite the near-perfect in-line positioning of the oxygen atom, thus preventing catalysis. Because of the near-perfect atomic positioning of the 2' oxygen atom relative to the phosphate group, orbital steering effects in this case are fortuitously uncoupled from conformational, distance and orientation effects, allowing an assessment of the catalytic power due purely to orbital steering. In contrast, a conformational change at the cleavage site is required to bring the 2' oxygen atom and the scissile phosphate group into atomic positions amenable to an in-line attack mechanism. In addition, the conformationally changed structure must then steer the lone-pair orbitals of the correctly positioned 2' oxygen atom toward the scissile phosphorus atom in order for cleavage to take place. We estimate that fulfillment of each of these two required changes may contribute separately an approximately 1000-fold rate enhancement, potentially accounting for a significant fraction of the catalytic power of this ribozyme. Orbital steering therefore appears to be a general phenomenon that may help to explain catalysis in both ribozymes and protein enzymes in a unified manner.

Estimated number of cases of foodborne infectious disease in New Zealand.

AIMS: To estimate the annual number of cases of infectious intestinal disease caused by foodborne pathogens in New Zealand and estimate the impact of these diseases in terms of days lost to illness. METHODS: Incidence of foodborne diseases were derived from data from infectious disease surveillance and hospital sources, and estimates of unreported illnesses using published population based studies. RESULTS: The estimated number of cases of foodborne infectious disease is approximately 119 000 per year, including 19 000 general practitioner visits, 400 hospital admissions, 22 cases of long term illness and two deaths. It is estimated that the number of cases of potentially foodborne infectious disease is approximately 199 000. Total number of cases of all infectious intestinal disease could be as high as 823 000. Days of lost production and leisure time activities lost to foodborne infectious disease are estimated as approximately 497 000. CONCLUSION: Foodborne infectious diseases represent a major public health burden in terms of the number of cases and days lost to illness.

Economic cost to New Zealand of foodborne infectious disease.

AIMS: To estimate the annual economic cost to New Zealand of foodborne infectious disease. METHODS: Annual incidence rates were combined with unit cost data to derive estimates of the annual economic cost to society of each foodborne infectious disease. Market prices and wages were used as proxies for the unit costs of resource utilisations. A decision analytic model was developed to estimate the costs of each disease and to undertake sensitivity analysis. RESULTS: There are an estimated 119 320 episodes of foodborne infectious disease per year in New Zealand (3241 per 100 000 population). The total cost of these cases was $55.1 million ($462 per case) made up of direct medical costs of $2.1 million, direct non-medical costs of $0.2 million, indirect cost of lost productivity of $48.1 million, and intangible cost of loss of life of $4.7 million. Campylobacteriosis generated most of the costs. Lost productivity was the major cost component for all diseases. The total cost of potentially foodborne infectious disease was estimated to be $88.8 million. Broad estimates of additional costs due to cases of infectious intestinal diseases caused by non-foodborne pathogens or for which no pathogen is identified could raise the cost to $215.7 million. CONCLUSION: The findings imply that resources of $55 million could be devoted to prevention of foodborne infectious disease. Efforts should focus on lowering the incidence of campylobacteriosis as this disease accounts for most of foodborne illness costs.

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.

We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure. Subsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately perpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe several interactions with functional groups on these residues that have been identified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. These interactions may therefore be relevant to the hammerhead ribozyme reaction mechanism.

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.

BACKGROUND: Bacterial signal recognition particle (SRP), consisting of 4.5S RNA and Ffh protein, plays an essential role in targeting signal-peptide-containing proteins to the secretory apparatus in the cell membrane. The 4.5S RNA increases the affinity of Ffh for signal peptides and is essential for the interaction between SRP and its receptor, protein FtsY. The 4.5S RNA also interacts with elongation factor G (EF-G) in the ribosome and this interaction is required for efficient translation. RESULTS: We have determined by multiple anomalous dispersion (MAD) with Lu(3+) the 2.7 A crystal structure of a 4.5S RNA fragment containing binding sites for both Ffh and EF-G. This fragment consists of three helices connected by a symmetric and an asymmetric internal loop. In contrast to NMR-derived structures reported previously, the symmetric loop is entirely constituted by non-canonical base pairs. These pairs continuously stack and project unusual sets of hydrogen-bond donors and acceptors into the shallow minor groove. The structure can therefore be regarded as two double helical rods hinged by the asymmetric loop that protrudes from one strand. CONCLUSIONS: Based on our crystal structure and results of chemical protection experiments reported previously, we predicted that Ffh binds to the minor groove of the symmetric loop. An identical decanucleotide sequence is found in the EF-G binding sites of both 4.5S RNA and 23S rRNA. The decanucleotide structure in the 4.5S RNA and the ribosomal protein L11-RNA complex crystals suggests how 4.5S RNA and 23S rRNA might interact with EF-G and function in translating ribosomes.

Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?

We have constructed a model structure that we believe represents the strongest possible physically and chemically reasonable representation of a hypothesized catalytically active hammerhead ribozyme structure in which a single divalent metal ion bridges the A9 and scissile phosphate groups. It has been proposed that such a structure arises from a conformational change in which the so-called ground-state structure (as observed by X-ray crystallography) rearranges in such a way that the pro-R oxygen atoms of both the A9 and scissile phosphate groups are directly coordinated by a single divalent metal ion in the transition-state of the hammerhead ribozyme cleavage reaction. We show that even the small subset of possible model structures that are consistent with these requirements, and that are stereochemically and sterically reasonable, are contradicted by experimental evidence. We also demonstrate that even a minimal subset of assumptions, i.e. that stems I and II are helical and that the two phosphate groups are coordinated by a divalent metal ion in the standard octahedral geometry, are sufficient to lead to this contradiction. We therefore conclude that such a mechanism of hammerhead ribozyme catalysis is untenable, at least in its present formulation.

RNA structure, metal ions, and catalysis.

Several new and unexpected insights into the metalloenzymology of ribozymes have been achieved in the past year. From a mechanistic point of view, the NMR and crystal structures of a small Pb(2+)-dependent ribozyme have been particularly revealing.

Derivatization of thymine and thymine photodimers with 4-bromomethyl-7-methoxycoumarin for fluorescence detection in high-performance liquid chromatography.

Exposure of DNA to utraviolet radiation results in the formation of a number of photoproducts, including thymine photodimers. A sensitive and selective analytical method based on high-performance liquid chromatography (HPLC) and fluorescent labeling with 4-bromomethyl-7-methoxycoumarin has been developed to quantify both thymine and thymine photodimers. The identity of the thymine and thymine dimer derivatives were determined by HPLC-electrospray ionization mass spectrometry. The derivatization reaction yield was maximized by optimizing several reaction variables. The limit of detection for HPLC method was 1.0 pmol thymine and 0.4 pmol thymine dimer for S/N = 3.

Cost comparison of antibacterial therapies for serious infections. A New Zealand 3-hospital study.

OBJECTIVE: The first aim was to identify and determine the economic costs of the regimens currently used in 3 New Zealand hospitals in the treatment of bacterial infections in haematology patients with febrile neutropenia and in intensive care patients with severe infections. The second was to develop a spreadsheet-based decision analytic model for use by hospital decision-makers as an aid in evaluating the comparative cost of drug regimens. DESIGN AND SETTING: The research utilised time and motion and microcosting techniques. The analytical perspective adopted for the study was that of a hospital administrator or clinical manager. PATIENTS AND INTERVENTIONS: Patients were eligible for inclusion in the study if either they were treated with the imipenem/cilastatin monotherapy, or could have been treated with this regimen. The final analysis considered 360 patient-treatment days and 8 antibacterials. MAIN OUTCOME MEASURES AND RESULTS: Drug acquisition cost ranged from 4.52 New Zealand dollars ($NZ; 1997 values) per patient-treatment day for gentamicin to $NZ104.81 for imipenem. The cost per patient-treatment day (when other cost components such as fluid additives, giving sets and needles were added) ranged from $NZ8.75 for gentamicin to $NZ129.12 for tazobactam. Drug acquisition cost, as a percentage of total drug preparation and administration cost, ranged from 52% for gentamicin to 93% for piperacillin. Giving sets and intravenous (i.v.) fluids were found to be important cost items when they were required specifically for the treatment regimen. There was a mean monitoring rate of 0.40 at a cost of $NZ6.41 per patient-treatment day for gentamicin. It was estimated that nephrotoxicity could add between $NZ23 and $NZ43 per day to the cost of aminoglycoside treatment. CONCLUSIONS: Although the small sample sizes of the study mean that results should be regarded as indicative rather than conclusive, there were sufficient information to construct a working model and show how the total cost of an antibacterial regimen could be evaluated in practical terms. The important cost drivers were found to be drug cost, the use of fluids and giving sets, and monitoring.

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone.

BACKGROUND: The catalytic activity of RNA enzymes is thought to require divalent metal ions, which are believed to facilitate RNA folding and to play a direct chemical role in the reaction. RESULTS: We have found that the hammerhead, hairpin and VS ribozymes do not require divalent metal ions, their mimics such as [Co(NH3)6]3+, or even monovalent metal ions for efficient self-cleavage. The HDV ribozyme, however, does appear to require divalent metal ions for self-cleavage. For the hammerhead, hairpin and VS ribozymes, very high concentrations of monovalent cations support RNA-cleavage rates similar to or exceeding those observed in standard concentrations of Mg2+. Analysis of all reaction components by inductively coupled plasma-optical emission spectrophotometry (ICPOES) and the use of a variety of chelating agents effectively eliminate the possibility of contaminating divalent and trivalent metal ions in the reactions. For the hairpin ribozyme, fluorescence resonance energy transfer experiments demonstrate that high concentrations of monovalent cations support folding into the catalytically proficient tertiary structure. CONCLUSIONS: These results directly demonstrate that metal ions are not obligatory chemical participants in the reactions catalysed by the hammerhead, hairpin, and VS ribozymes. They permit us to suggest that the folded structure of the RNA itself contributes more to the catalytic function than was previously recognised, and that the presence of a relatively dense positive charge, rather than divalent metal ions, is the general fundamental requirement. Whether this charge is required for catalysis per se or simply for RNA folding remains to be determined.

The structural basis of hammerhead ribozyme self-cleavage.

We have captured an 8.7 A conformational change that takes place in the cleavage site of the hammerhead ribozyme during self-cleavage, using X-ray crystallography combined with physical and chemical trapping techniques. This rearrangement brings the hammerhead ribozyme from the ground state into a conformation that is poised to form the transition state geometry required for hammerhead RNA self-cleavage. Use of a 5'-C-methylated ribose adjacent to the cleavage site permits this ordinarily transient conformational change to be kinetically trapped and observed crystallographically after initiating the hammerhead ribozyme reaction in the crystal. Cleavage of the corresponding unmodified hammerhead ribozyme in the crystal under otherwise identical conditions is faster than in solution, indicating that we have indeed trapped a catalytically relevant intermediate form of this RNA enzyme.

Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.

Terbium(III) [Tb(III)] was shown to inhibit the hammerhead ribozyme by competing with a single magnesium(II) ion. X-ray crystallography revealed that the Tb(III) ion binds to a site adjacent to an essential guanosine in the catalytic core of the ribozyme, approximately 10 angstroms from the cleavage site. Synthetic modifications near this binding site yielded an RNA substrate that was resistant to Tb(III) binding and capable of being cleaved, even in the presence of up to 20 micromolar Tb(III). It is suggested that the magnesium(II) ion thought to bind at this site may act as a switch, affecting the conformational changes required to achieve the transition state.

RNA catalysis.

Our understanding of the relationship between the structure of RNA and its catalytic activity has advanced significantly in the past year. These advances include time-resolved crystallographic studies on the hammerhead ribozyme, as well as new structures of a group I intron, a lead(II)-cleavage ribozyme, a hepatitis delta virus ribozyme, and components of the spliceosome machinery and the peptidyl transferase center of the ribosome and, most significantly, the structure of the ribosome itself.

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH-ion is located between two Mg2+ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'- endo to the C2'- endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH-ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH-ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA.

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.

The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.