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A McPherson

Publications and source records attributed to A McPherson.

At least 37 records · Page 2Linked to original sources
PubMed2002

Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology.

Atomic force microscopy (AFM) investigation revealed the sources of disorder and mechanisms of their formation in crystals of an icosahedral plant virus, Cucumber Mosaic Virus (CMV) and structure of the Herpes Simplex Virus (HSV-1). The combination of defects and local disorder in CMV crystals presented here are likely the physical bases for mosaicity in virus crystals, and may be largely responsible for their limited diffraction resolution. High-resolution images of intact, enveloped HSV-1 and the underlying capsid structure demonstrate capabilities of AFM to probe structures of large macromolecular assemblies.

Capsid↗
PubMed2002

Is 'watchful waiting' a real choice for men with prostate cancer? A qualitative study.

OBJECTIVE: To understand what leads men to choose 'watchful waiting' rather than active treatment for cancer of the prostate. PATIENTS AND METHODS: Fifty men with confirmed prostate cancer in England, Wales and Scotland were interviewed about all aspects of their illness, for a Database of Individual Patients' Experience of illness. The sample included men at different stages of diagnosis and with experience of a wide range of treatments. We report here only what men said about their choice of treatment and the decision-making process. RESULTS: Watchful waiting would have been clinically inappropriate for almost half of the men (those with serious urinary symptoms and those with metastatic disease). However, few of the men who might have chosen watchful-waiting remembered this being presented as a serious option. Most in this group chose radical prostatectomy, radiotherapy, brachytherapy or cryosurgery. The few who chose watchful waiting had found doctors who supported their decision, had assessed the evidence from Internet sites, and were concerned about the side-effects and uncertain outcome of treatment. Men who chose watchful waiting, as well as those who opted for treatment, described considerable pressure from family members, doctors or support groups, to seek active treatment. CONCLUSION: This study helps to explain why some men will not contemplate watchful waiting, and why others may find it difficult to pursue that option. Understanding men's concerns may help clinicians to support men's treatment decisions. Treatment for prostate cancer is highly controversial because no randomized, controlled trials have shown whether or not active intervention increases survival. If trials are not completed it cannot be determined whether active treatments are the best course of action for men with prostate cancer.

Aged↗
PubMed2001

Self-repair of biological fibers catalyzed by the surface of a virus crystal.

Helical fibers, presumably proteinaceous and of microbial origin, have been visualized by atomic force microscopy on the surfaces of crystals of satellite tobacco mosaic virus. If the crystals are growing, then the fibers are incorporated intact into the crystal lattice. If broken on the crystal surface, then within a few minutes, the fibers self-reassemble to reestablish continuity. This, we believe, is the first observation of such a crystal surface-catalyzed repair of a biological structure. The surfaces of virus crystals provide ideal workbenches for the visualization and manipulation of nanoscale objects, particularly extended structures such as these fibers.

Catalysis↗
PubMed2001

Crystallization of Brome mosaic virus and T = 1 Brome mosaic virus particles following a structural transition.

Brome mosaic virus (BMV), a T = 3 icosahedral plant virus, can be dissociated into coat protein subunits and subunit oligomers at pH 7.5 in the presence of concentrated salts. We have found that during the course of this treatment the coat protein subunits are cleaved, presumably by plant cell proteases still present in the preparation, between amino acids 35 and 36. The truncated protein subunits will then reorganize into T = 1 icosahedral particles and can be crystallized from sodium malonate. Quasi elastic light scattering and atomic force microscopy results suggest that the transition from T = 3 to T = 1 particles can occur by separate pathways, dissociation into coat protein subunits and oligomers and reassembly into T = 1 particles, or direct condensation of the T = 3 virions to T = 1 particles with the shedding of hexameric capsomeres. The latter process has been directly visualized using atomic force microscopy. Native T = 3 virions have been crystallized in several different crystal forms, but neither a rhombohedral form nor either of two orthorhombic forms diffract beyond about 3.4 A. Tetragonal crystals of the T = 1 particles, however, diffract to at least 2.5 A resolution. Evidence suggests that the T = 1 particles are more structurally uniform and ordered than are native T = 3 virions. A variety of anomalous virus particles having diverse sizes have been visualized in preparations of BMV used for crystallization. In some cases these aberrant particles are incorporated into growing crystals where they are frequently responsible for defect formation.

Bromovirus↗
PubMed2001

Atomic force microscopy applications in macromolecular crystallography.

Atomic force microscopy (AFM) can be applied both in situ and ex situ to study the growth of crystals from solution. The method is particularly useful for investigating the crystallization of proteins, nucleic acids and viruses because it can be carried out in the mother liquor and in a non-perturbing fashion. Interactions and transformations between various growth mechanisms can be directly visualized as a function of supersaturation, as can the incorporation of diverse impurities and the formation and propagation of defects. Because the crystals can be observed over long periods, it is also possible to obtain precise quantitative measures of the kinetic parameters for nucleation and growth. Finally, AFM has allowed us to identify a number of previously unsuspected phenomena that influence nucleation, rate of growth and the ultimate perfection of macromolecular crystals. These are all features which are important in determining the ultimate resolution and quality of a crystal's diffraction pattern.

Crystallization↗
PubMed2001

Structural transitions of satellite tobacco mosaic virus particles.

Satellite tobacco mosaic virus (STMV) can undergo at least two physical transitions that significantly alter its mechanical and structural characteristics. At high pH the 17-nm STMV particles expand radially by about 5 A to yield particles having diameters of about 18 nm. This pH-induced transition is further promoted by aging of the virions and degradation of the RNA, so that swollen particles ultimately appear even at neutral pH. While the native 17-nm particles crystallize as orthorhombic or monoclinic crystals which diffract to high resolution (1.8 A), the enlarged 18-nm particles crystallize in a cubic form which diffracts to no better than 5 A. In the transition, not only do the capsid protein subunits move radially outward, but the helical RNA segments with which they interact do as well. This is noteworthy because it demonstrates that the RNA and the protein shell are capable of coordinated movement, and that neither structure is rigidly defined or independent of the other. Using atomic force microscopy, it can be shown that STMV particles, upon drying, lose their mechanical rigidity and undergo deformation. Virions initially 17 nm in diameter shrink to more uniform final sizes than do 18 nm, initially swollen particles. This transition appears to be irreversible, as the particles do not reassume their former size nor structural rigidity upon rehydration. Evidence is also presented that preparations of native virus and their crystals are naturally somewhat heterogeneous and contain a variety of particles of anomalous size.

Crystallization↗
PubMed2001

X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin.

The structure of canavalin, the vicilin-class storage protein from jack bean, was refined to 1.7 A resolution in a highly twinned rhombohedral crystal of space group R3 and unit-cell parameters a = b = c = 83.0 A, alpha = beta = gamma = 111.1 degrees. The resulting R and R(free) were 0.176 and 0.245, respectively. The orthorhombic crystal structure (space group C222(1), unit-cell parameters a = 136.5, b = 150.3, c = 133.4 A) was also refined with threefold non-crystallographic symmetry restraints. R and R(free) were 0.181 and 0.226, respectively, for 2.6 A resolution data. No significant difference in the protein structure was seen between these two crystal forms, nor between these two and the hexagonal and cubic crystal forms reported elsewhere [Ko et al. (1993), Acta Cryst. D49, 478-489; Ko et al. (1993), Plant Physiol. 101, 729-744]. A phosphate ion was identified in the lumen of the C-terminal beta-barrel. Lattice interactions showed that the trimeric molecule could be well accommodated in both 'top-up' and 'bottom-up' orientations in a rhombohedral unit cell of the R3 crystal and explained the presence of a high twin fraction. The large inter-trimer stacking interface of the C222(1) crystal may account for its relative stability. Atomic force microscopy (AFM) investigations of the growth of three crystal forms of canavalin indicate the rhombohedral form to be unique. Unlike the other two crystal forms, it contains at least an order of magnitude more screw dislocations and stacking faults than any other macromolecular crystal yet studied, and it alone grows principally by generation of steps from the screw dislocations. The unusually high occurrence of the screw dislocations and stacking faults is attributed to mechanical stress produced by the alternate molecular orientations in the rhombohedral crystals and their organization into discrete domains or blocks. At boundaries of alternate domains, lattice strain is relieved by the formation of the screw dislocations.

Crystallization↗
PubMed2001

Biophysical studies on the RNA cores of satellite tobacco mosaic virus.

Satellite tobacco mosaic virus (STMV) was probed using a variety of proteases. Consequences of the degradation were analyzed using gel electrophoresis, quasi-elastic light scattering (QELS), and atomic force microscopy (AFM). Proteolysis rates of 30 minutes for complete degradation of the protein capsid, up to many hours, were investigated. With each protease, degradation of virions 17 nm in diameter was shown by QELS to result in particles of 10 nm diameter, which is that of the RNA core observed in the virion by x-ray diffraction analysis. This was verified by direct visualization with atomic force microscopy. Using QELS, it was further shown that freshly prepared RNA cores remain as individual, stable, 10-nm condensed particles for 12 to 24 h. Clusters of particles then formed, followed by very large aggregates of 500 to 1000 nm diameter. AFM showed that the aggregates were composed of groups of the condensed RNA cores and were not due to unfolding of the nucleic acid. No unfolding of the core particles into extended conformation was seen by AFM until the samples were heated well beyond 90 degrees C. Mass spectrometry of RNA core particles revealed the presence of a major polypeptide whose amino acid sequence corresponded to residues 2 through 25 of the coat protein. Amino acids 13 through 25 were previously observed to be in direct contact with the RNA and are presumably protected from protease digestion. Low resolution difference Fourier analyses indicated the courses of the remainders of the amino terminal strands (amino acids 2-12) in intact virions. Any individual strand appears to have several choices of path, which accounts for the observed disorder at high resolution. These positively charged strands, serving as virtual polyamines, engage the helical segments of RNA. The intimate association of amino acid residues 2 through 25 with RNA likely contributes to the stability of the condensed conformation of the nucleic acid cores.

Biophysical Phenomena↗
PubMed2001

Satellite tobacco mosaic virus RNA: structure and implications for assembly.

The initial appearance of 45% of the single-stranded RNA of satellite tobacco mosaic virus in electron density maps suggested the entire RNA conformation could be delineated. Subsequent work has localized nearly 80% of the RNA as stem-loop elements. Connection of the stem-loops in the most efficient manner produces a persuasive model for the encapsidated RNA. This arrangement has significant implications for virus assembly and for the essential role of RNA.

Computer Simulation↗
PubMed2001

Outpatient cognitive behavioural therapy programme for alcohol dependence: impact of naltrexone use on outcome.

OBJECTIVE: Cognitive-behavioural therapy (CBT) has been effectively used in the treatment of alcohol dependence. Clinical studies report that the anticraving drug naltrexone, is a useful adjunct to treatment. Currently, few data are available on the impact of adding this medication to programmes in more typical, outpatient, and rehabilitation settings. The objective of this study was to examine the impact on outcome of adding naltrexone to an established outpatient alcohol rehabilitation program which employed CBT. METHOD: Fifty patients participated in an established 12-week, outpatient, 'contract'-based alcohol abstinence programme which employed CBT. They also received naltrexone 50 mg orally daily (CBT + naltrexone). Outcomes were compared with 50 historical, matched controls, all of whom participated in the same programme without an anticraving medication (CBT alone). All patients met DSM-IV criteria for alcohol dependence. RESULTS: Programme attendance across the eight treatment sessions was lower in the CBT alone group (p < 0.001). Relapse to alcohol use occurred sooner and more frequently in the CBT alone group (p < 0.001). Rehabilitation programme completion at 12 weeks was 88% (CBT + naltrexone) compared with 36% for (CBT alone) (p < 0.001). Alcohol abstinence at 12 weeks was 76% (CBT + naltrexone) compared with 18% (CBT alone) (p < 0.001). CONCLUSION: When employing the same outpatient rehabilitation programme and comparing outcomes using matched historical controls, the addition of naltrexone substantially improves programme attendance, programme completion and reported alcohol abstinence. In a typical outpatient programme, naltrexone addition was associated with significantly improved programme participation, better outcomes and was well tolerated.

Adult↗
PubMed2001

Randomized controlled trial of two cigarette quit programmes in coronary care patients after acute myocardial infarction.

BACKGROUND: Tobacco cessation after acute myocardial infarction (AMI) substantially improves outcome but how effective individual programmes are needs to be established. To date, few studies have examined this factor. AIMS: To assess the outcome of two smoking cessation programmes after AMI. METHODS: One hundred and ninety-eight current smokers admitted to coronary care with an AMI participated in a randomized controlled study comparing two outpatient tobacco interventions, the Stanford Heart Attack Staying Free (SF) programme and a Usual Care (UC) programme. RESULTS: Log-rank analyses revealed that patients in the SF programme were retained longer (P < 0.001) and had higher cotinine validated abstinence rates (P < 0.001) compared with patients in the UC programme. Twelve months after intervention, 39% of the SF programme compared with 2% of the UC programme demonstrated cotinine validated tobacco cessation, representing a significant reduced relapse rate in the SF programme (chi2, P< 0.001). CONCLUSIONS: The SF smoking cessation programme initiated in hospital can significantly reduce smoking rates at 12 months after myocardial infarction. Although superior to the UC quit programme, Australian outcomes were lower than the American programme originators' published outcomes.

Adult↗
PubMed2001

A comparison of salts for the crystallization of macromolecules.

Thirty-one proteins and viruses that we knew from our own experience could be crystallized, or had been reported to have been crystallized by others, were investigated. In this experiment, each protein or virus was subjected to a crystallization screen of 12 different salts, each titrated to pH 7.2 beforehand, at concentrations ranging from 20% saturation to 90% saturation. Eight macromolecules failed to crystallize at all from any salt and were omitted from consideration. From the remaining 23 proteins, each salt was scored according to how many proteins and viruses it successfully crystallized. Among several results, one was particularly striking. Sodium malonate clearly was much more successful than any other salt, resulting in the crystallization of 19 of the 23 macromolecules, almost twice as effective as the next most successful salt, which was a draw between sodium acetate, sodium tartrate, sodium formate, and ammonium sulfate (11 of 22). The high success rate of sodium malonate in producing crystals was even more impressive when an overall unique success rate with individual macromolecules was considered.

Ammonium Sulfate↗
PubMed2000

Atomic force microscopy studies of icosahedral virus crystal growth.

Biological macromolecules and particularly viruses, provide excellent systems for the study of crystallization from solution because of their relatively large size. The kinetics of their crystallization is at least an order of magnitude less than for conventional systems, and their large size permits visualization, both of crystal lattices and individual particles, by techniques such as atomic force microscopy (AFM). This technique is especially powerful for biological macromolecules because it can be utilized in situ, in the crystallization mother liquor, over long periods of time without perturbing the growing crystals. We present here observations using AFM of the nucleation and growth of crystals of satellite tobacco mosaic virus, and some recordings as well of bromegrass mosaic virus. Correlations are made, where possible, with corresponding analyses using X-ray diffraction analysis.

Journal Article↗