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C Nave

Publications and source records attributed to C Nave.

At least 19 recordsLinked to original sources
PubMed2002

Automation of the collection and processing of X-ray diffraction data -- a generic approach.

With modern detectors and synchrotron sources, it is now routine to collect complete data sets in 10-30 min. To make the most efficient use of these resources, it is desirable to automate the collection and processing of the diffraction data, ideally to a level at which multiple data sets can be acquired without any intervention. A scheme is described to allow fully automated data collection and processing. The design is modular, so that it can easily be interfaced with different beamline-control programs and different data-processing programs. An expert system provides a communication path between the data-processing software and the beamline-control software and takes decisions about the data collection based on project information provided by the user and experimental data provided by the data-processing program.

Algorithms↗
PubMed2001

X-ray diffraction from DNA fibres under tension.

When DNA fibres are stretched during drying, the polymer undergoes a conformational transition. We present quantitative results from X-ray diffraction studies on such fibres held at various ambient relative humidities. These indicate that the molecules are arranged in arrays which are crystalline in projection down the fibre axis. The packing can be explained in terms of a hexagonal cell with a lattice parameter, a, of approximately 13 A which varies with humidity. The patterns contain meridional intensities at 1/3.4 A(-1) and 1/6.5 A(-1), a strong off-meridional intensity at Z=1/5.6 A(-1) and diffuse scatter at Z=1/28 A(-1).

Animals↗
PubMed1999

Matching X-ray source, optics and detectors to protein crystallography requirements.

A review of the requirements for collecting X-ray diffraction data from protein crystals is given, with an emphasis on the properties of the crystal and its diffraction pattern. The size, unit-cell dimensions and perfection of the crystals can all be related to the required size and divergence of the incident X-ray beam, together with the size and spatial resolution of the detector. The X-ray beam causes primary radiation damage, even in frozen crystals. If the incident beam is very intense, temperature rises and gradients could occur in the crystal. The extent to which these problems can be overcome is also discussed.

Crystallization↗
PubMed1998

A description of imperfections in protein crystals.

An analysis is given of the contribution of various crystal imperfections to the rocking widths of reflections and the divergence of the diffracted beams. The crystal imperfections are the angular spread of the mosaic blocks in the crystal, the size of the mosaic blocks and the variation in cell dimensions between blocks. The analysis has implications for improving crystal perfection, defining data-collection requirements and for data-processing procedures. Measurements on crystals of tetragonal lysozyme at room temperature and 100 K were made in order to illustrate how parameters describing the crystal imperfections can be obtained. At 100 K, the dominant imperfection appeared to be a variation in unit-cell dimensions in the crystal.

Crystallization↗
PubMed1998

Source, optical and detector requirements for X-ray diffraction and scattering.

The standard curves used to describe the properties of synchrotron radiation sources usually consist of a plot of the flux or brightness from the source as a function of wavelength. These curves are useful for the case where a high flux or brightness is required. Many experiments do not fall into this category. An alternative description of the source requirements is to provide the maximum flux into the phase space volume defined by the specimen. A diagrammatic way of illustrating how this can be achieved is derived. This illustrates how the source, optics and detectors can be matched to the requirements of a particular experiment. This approach is illustrated using, as examples, a beamline on the SRS and two beamlines planned for DIAMOND, the proposed new UK third-generation source.

Journal Article↗
PubMed1998

Beamline 14: a new multipole wiggler beamline for protein crystallography on the SRS.

A new multipole wiggler device has been designed for the 2.0 GeV Synchrotron Radiation Source at Daresbury Laboratory in the UK. The nine-pole 2.0 T device will provide radiation for two beamlines dedicated to protein crystallography, one of which will be of high intensity. This article provides details of the design of the two stations and outlines methods being developed to combine dealing with the high heat load from the radiation while allowing both stations to be built as close to the centre of the fan as possible.

Journal Article↗
PubMed1996

[The electrophysiological bases of aberrant intraventricular conduction during atrial fibrillation].

Twenty-four hours electrocardiogram from 4 patients with chronic atrial fibrillation and intraventricular aberrant conduction were analyzed. Aim of the study was to evaluate the reliability of the Ashman's and Akthar's rules in electrocardiographic differential diagnosis between aberrancy and ectopy. We computed parameters related to 10 RR interval preceding the aberrant conduction (AB+ Group), normal complex QRS (AB-Group) and ectopic QRS (E Group): coupling interval (CI), preceding CI cycle (PCL1), preceding PCL1 cycle (PCL2), the difference between PCL1 an PCL2 (delta PCL1), the difference between CI an PCL1 (delta CI), the mean value (RR10) and the standard deviation (RR10SD) of the 10 QRS complexes preceding the end of the sequence. Specificity of Akthar's rule was 48.7% (range 45-50%), sensibility was 90.1% (range 75-100%). PCL2, delta PCL1 and RR10DS were significantly different between AB+ and AB- Group but not between AB+, AB- and E Group. In this work Akthar's rule showed a better reliability than Ashman's rule but specificity was low (probably related to concealed conduction in atrio-ventricular node). RR10DS, but not RR10, were significantly higher in AB+ Group than AB- Group suggesting that acceleration of the cycle length can provoke CVA by increasing the difference between the refractory period of His bundle branches. Aberrant ventricular conduction cannot be determined by a mathematical rule. In the differential diagnosis of wide QRS during atrial fibrillation only morphological analysis of QRS and the study of coupling interval and compensatory pause are helpful.

Atrial Fibrillation↗
PubMed1995

Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data.

The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the alpha-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.

Journal Article↗
PubMed1995

Matching electrostatic charge between DNA and coat protein in filamentous bacteriophage. Fibre diffraction of charge-deletion mutants.

The virion of Ff (fd, f1, M13) filamentous bacteriophage consists of a long tube of coat protein subunits in a shingled, helical array, surrounding a genome of circular single-stranded DNA. Modified fd virions have been generated by a mutation (K48A) that removes one positive charge from each coat protein subunit in the C-terminal region of the polypeptide chain facing the DNA. The number of nucleotides in the mutant DNA is unchanged, but the K48A virions are 35% longer than wild-type. We have measured the X-ray diffraction attributable to single virions in hydrated gels of wild-type and K48A bacteriophages. Most of the diffraction pattern shows no significant difference between wild-type and K48A. Since the DNA is only about 12% by weight of the wild-type virion, the diffraction pattern is dominated by the protein contribution, and the absence of significant differences indicates that there are no significant changes in the symmetry or structure of the protein coat. But there is a change in the diffraction pattern in a region where the DNA and protein contributions are comparable. The diffraction pattern of the K48A mutant shows an increase in intensity of one of the weaker equatorial peaks, relative to wild-type, in a region where the protein contribution has negative sign but the DNA contribution has positive sign. This is consistent with a decrease in the ratio of DNA:protein per unit length of the K48A mutant. The results support the view that the protein forms a sheath lined with positive charges interacting electrostatically and non-specifically with a negatively charged DNA core of matching charge density. The lower positive charge density lining the capsid in the K48A mutant means that correspondingly fewer nucleotides can be packaged per coat protein subunit, which in turn requires an elongation of the DNA inside the virion. A longer virion is thus required to package the same amount of DNA. Within the error of measurement, the number of positive charges on the protein interacting with the DNA is the same in K48A as in the wild-type, despite the fact that the mutant is 35% longer than the wild-type.

Capsid↗
PubMed1994

Radiation damage in protein crystals at low temperature.

This paper describes the study of the effects of radiation damage on the quality of data collected from a protein crystal at 100 K. It is shown that radiation damage causes measurable effects in the diffraction pattern. This implies that, even at liquid nitrogen temperatures, there is a limit to the size of a crystal from which a complete data set can be collected.

Journal Article↗
PubMed1994

Data collection at short wavelengths in protein crystallography.

The development of high-intensity X-ray sources and the use of insertion devices will make it possible to collect data routinely from protein crystals at very short wavelengths (lambda </= 0.5 A). Possible benefits of using shorter wavelengths can be inferred from the improvement in the quality of the data when using a wavelength lambda approximately 0.9 A instead of one close to the Cu Kalpha emission edge. In addition to fewer absorption errors, two factors might contribute to this improvement. These are an increase in the lifetime of the protein crystal and a better signal-to-background ratio. In this paper we address the second of these. In order to compare the quality of the data and the relative background level in the diffraction patterns at different wavelengths two data sets have been collected at lambda = 0.92 and 0.55 A. The results obtained from data processing and careful measurement of the background in the raw images suggest that, in the absence of absorption errors and radiation damage, data collection at very short wavelengths does not provide higher quality data. There is no improvement in the signal-to-background ratio in the short-wavelength data.

Journal Article↗
PubMed1994

Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe.

The filamentous bacteriophages are flexible rods about 1 to 2 microns long and 6 nm in diameter, with a helical shell of protein subunits surrounding a DNA core. The approximately 50-residue coat protein subunit is largely alpha-helix and the axis of the alpha-helix makes a small angle with the axis of the virion. The protein shell can be considered in three sections: the outer surface, occupied by the N-terminal region of the subunit, rich in acidic residues that interact with the surrounding solvent and give the virion a low isoelectric point; the interior of the shell, including a 19-residue stretch of apolar side-chains, where protein subunits interact mainly with each other; and the inner surface, occupied by the C-terminal region of the subunit, rich in basic residues that interact with the DNA core. The fact that virtually all protein side-chain interactions are between different subunits in the coat protein array, rather than within subunits, makes this a useful model system for studies of interactions between alpha-helix subunits in a macromolecular assembly. We describe molecular models of the class I filamentous bacteriophages. This class includes strains fd, f1, M13 (these 3 very similar strains are members of the Ff group), If1 and IKe. Our model of fd has been refined to fit quantitative X-ray fibre diffraction data to 30 A resolution in the meridional direction and 7 A resolution in the equatorial direction. A simulated 3.3 A resolution diffraction pattern from this model has the same general distribution of intensity as the experimental diffraction pattern. The observed diffraction data at 7 A resolution are fitted much better by the calculated diffraction pattern of our molecular model than by that of a model in which the alpha-helix subunit is represented by a rod of uniform density. The fact that our fd model explains the fd diffraction data is only part of our structure analysis. The atomic details of the model are supported by non-diffraction data, in part previously published and in part newly reported here. These data include information about permitted or forbidden side-chain replacements, about the effect of chemical modification, and about spectroscopic experiments.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1994

[Infectious endocarditis in dentistry practice: recent controversies and modes of the use of antibiotic prophylaxis].

A survey by questionnaire to assess the daily practice of the antibiotic prophylaxis of infective endocarditis by physicians attending post-graduate schools of the Institutes of Oral Surgery and Stomatology (Group A n = 83) and Cardiology (Group B n = 46) of the Second University of Naples has been conducted. They were asked about dental procedure and cardiopathies that require prophylaxis for infective endocarditis, the relationship between infective endocarditis and rheumatic disease and the provision of antibiotic. Extraction of tooth and dental and oral surgery have been reported as the most risky procedures. Moreover provision of antibiotic prophylaxis was suggested to patients not at risk (pacemaker or coronary artery bypass), and was not suggested in high risk conditions (mitral valve prolapse with regurgitation and hypertrophic cardiomyopathy). Most of the 50-60% practitioners usually start the prophylaxis 24-48 hours before the procedure and prolong it for 48-72 hours. These results underline the need for improvement of the knowledge for the antibiotic prophylaxis of infective endocarditis.

Anti-Bacterial Agents↗
PubMed1994

[Surgical treatment of incessant atrial tachycardia: description of a case].

A 50 year old woman with no evidence of structural heart disease was referred for ectopic incessant repetitive atrial tachycardia uncontrolled by medical therapy. Intracavitary and transesophageal simultaneous recordings revealed the earliest atrial electrical activity to be located in the left atrium. Intraoperative electrophysiologic mapping demonstrated that the site of earliest atrial activation was in a small diverticulum of the left atrial appendage. Excision of the appendage and isolation of left atrium was carried out with restoration of sinus rhythm. The patient was arrhythmia-free till 24 months later. Surgical treatment appears to be an effective therapeutic option for drug-resistant ectopic atrial tachycardia.

Electrocardiography↗
PubMed1994

[Double ventricular response to a single atrial stimulation caused by simultaneous anterograde conduction through two atrioventricular nodal pathways].

In a patient with atrioventricular nodal reentrant tachycardia, during programmed stimulation, an atrial extrastimulus induced a double ventricular response due to a single atrial depolarization, with simultaneous and delayed anterograde conduction through fast and slow pathways, and induced the tachycardia. Pacing-induced type I block involving both pathways put these pathways out of phase, so that the distal conduction system and the ventricle responded to both the fast and slow pathways anterograde impulses.

Atrioventricular Node↗
PubMed1993

[Linking in a phase-3 branch block: the electrocardiographic manifestations].

Two cases of phase 3 intraventricular block and linking phenomenon of type 1 and type 2 (or bigeminal rhythm linking) are presented. In the first case, complexes that follow the extrasystolic blocked beat are wide, although they are associated with relative long R-R cycle:type 1 linking. In the second case, bundle branch block and normal conduction alternate in bigeminal extrasystolic beats:type 2 linking. The linking phenomenon is due to concealed retrograde penetration of the bundle branch that is blocked in anterograde direction. It delays the cycle and the refractory period of the bundle branch. Therefore, in type 1 linking, the subsequent stimulus, although occurring with a long R-R cycle, is again blocked in the same bundle branch. In type 2 linking, the R-R cycle and refractory period, occurring after bundle branch block, are shorted because comprised between retrograde activation by extrastimulus and anterograde activation by subsequent sinus stimulus. The subsequent ectopic impulse, although premature, is normally conducted.

Adult↗
PubMed1992

[Slow and fast AV nodal pathways in tachycardia complicating Wolff-Parkinson-White syndrome: report of a case].

Electrophysiologic studies in a patient with intermittent ventricular pre-excitation revealed several types of paroxysmal narrow-QRS tachycardia (PSVT). One type of PSVT was characterized by normal retrograde atrial sequences with P waves occurring simultaneously with QRS. This type of PSVT reflected AV nodal reentry with anterograde slow pathway and retrograde fast pathway conduction. A second PSVT reflected alternation of anterograde fast and slow AV nodal pathway conduction and retrograde anomalous pathway conduction. A third PSVT reflected anterograde slow AV nodal pathway and retrograde anomalous pathway conduction. Moreover, discontinuous AV nodal conduction curves (A1A2/H1H2), characteristic of dual AV nodal pathway conduction, were obtained with programmed atrial extra stimulation. These observations suggest that dual AV nodal pathway conduction can coexist with abnormal bypass tract and can be the cause of PSVT in patients with Wolff-Parkinson-White syndrome.

Adult↗