Search PubMed⌕ Search

Biomedical subjects

J E Johnson

Publications and source records attributed to J E Johnson.

At least 19 recordsLinked to original sources
PubMed2006

Evaluation of a dual-arm Archimedean spiral array for microwave hyperthermia.

PURPOSE: This effort describes a third-party performance evaluation of a novel, commercial, dual-armed Archimedean spiral array hyperthermia applicator. The applicator is analysed for its ability to couple efficiently into muscle equivalent phantom loads, operate over a broad bandwidth to help accommodate variable tissue properties and generate predictable and repeatable SAR contours that are adaptable to clinically probable disease shapes. MATERIALS AND METHODS: Characterization of the applicator includes E-field and return-loss measurements in liquid muscle tissue-equivalent phantom, as well as comparison of 'treatment-planning' simulations of several possible array SAR patterns with measured SAR from non-coherently driven spiral array antennae. RESULTS: The applicator demonstrates a reasonably low return loss over a large bandwidth and the ability to generate a very uniform heating pattern. Ability to adjust SAR contours spatially to fit specific shapes is also demonstrated. CONCLUSIONS: This device should prove a welcome addition to a currently limited set of superficial heating applicators to provide controllable heating of superficial tissue disease.

Equipment Design↗
PubMed2005

Preliminary x-ray characterization of authentic providence virus and attempts to express its coat protein gene in recombinant baculovirus.

Providence Virus (PrV) is a non-envoloped, T = 4 icosahedral beta-tetravirus that undergoes autocatalytic cleavage of its coat protein precursor after capsid assembly. This is also a well characterized function of Nudaurelia capensis omega virus (NomegaV), a member of the related omegatetraviruses, whose x-ray structure has been determined. Virus-like particle (VLP) production of PrV in a recombinant baculovirus expression system was attempted to obtain high VLP yields for comparison of structural and autocatalytic active site properties between these virus groups. This resulted in insoluble aggregates of PrV coat protein even though NomegaV VLPs have been successfully produced in the same system. Betatetraviruses may be more dependent on compartmentalization and availability of their full-length genome for proper folding and assembly. However, crystals were grown of limited quantities of authentic PrV produced in cell culture and a partial X-ray data set collected to 3.8 A resolution. The virus particle position and orientation in the unit cell was determined by space group consideration and rotation function analysis. A phasing model, based on NomegaV, was developed to initiate the structure solution of PrV.

Baculoviridae↗
PubMed2005

Preoperative evaluation of live renal donors using multislice CT angiography.

AIM: To determine the accuracy of multidetector row CT renal angiography in the preoperative evaluation of live kidney donors, and to identify potential pitfalls when reporting. METHODS: Between July 1998 and June 2003, 74 consecutive live renal donors underwent contrast-enhanced multidetector row CT renal angiography before donor nephrectomy. The operative notes and radiological reports of all cases were reviewed retrospectively. Where a significant discrepancy was identified, the archived images were reviewed by two radiologists in the light of the intraoperative findings. RESULTS: A total of 12 discrepancies were identified in 11 of the 74 cases (15%). In the preoperative CT angiography reports, 4 accessory arteries, 6 early-branching renal arteries, 1 duplicated renal vein and 1 accessory ureter were not identified; 9 of these were evident on review, but were not detected at the time of reporting. In 3 cases (1 accessory artery, the duplicated renal vein and the accessory ureter), the anomaly was not visible on review of the CT angiographic data, even with the benefit of hindsight. Surgical feedback during the study period resulted in modifications to CT technique and improved performance. CONCLUSION: In the majority of cases, there was good correlation between preoperative CT renal angiography and operative findings. Most discrepancies were due either to an oversight by the reporting radiologist, or failure to fully appreciate the potential surgical significance of certain findings. Regular surgical feedback plays a valuable role in improving reporting accuracy and maintaining imaging standards.

Adult↗
PubMed2004

Tendon Achilles lengthening for the treatment of neuropathic ulcers causes a temporary reduction in forefoot pressure associated with changes in plantar flexor power rather than ankle motion during gait.

The purposes of this study were to determine the effects of tendon Achilles lengthening (TAL) on ambulatory plantar pressures and ankle range of motion, moment, and power, and to determine whether changes in forefoot pressure after treatment of a neuropathic ulcer are related to changes in ankle dorsiflexion range of motion (DFROM) or plantar flexor (PF) power during gait. Pressure and gait tests were performed before treatment, and at 3 weeks and 8 months after treatment in two randomly assigned groups of subjects with diabetes, equinus deformity, and a neuropathic forefoot ulcer treated with TAL and total contact casting (TAL group, n=14), or total contact casting alone (TCC group, n=14). The TAL group had an initial decrease in forefoot peak pressure (PP) (27%), forefoot pressure-time integral (PTI) (42%), PF moment (53%), and PF power (65%), along with an initial increase in rear foot PP (34%), rear foot PTI (48%), and DFROM (74%). Post-surgical changes in rear foot pressure and DFROM were maintained up to 8 months after treatment with TAL, whereas forefoot pressure and PF moment and power increased significantly. Changes in forefoot pressure after treatment in either group were correlated with changes in PF power (r=0.45-0.60), but not with changes in DFROM during gait (r=-0.02-0.08). Results suggest TAL causes a temporary reduction in forefoot pressure primarily by reducing PF power during gait. The initial decrease in forefoot pressure, followed by progressive reloading of forefoot tissues as PF muscles regain strength after TAL, may help reduce the risk of ulcer recurrence in patients with diabetes.

Achilles Tendon↗
PubMed2004

Virus stability and protein-nucleic acid interaction as studied by high-pressure effects on nodaviruses.

In this work, we evaluate the stability, dynamics and protein-nucleic acid interaction in Flock House virus (FHV). FHV is an RNA insect virus, non-enveloped, member of the family Nodaviridae. It is composed of a bipartite single-stranded RNA genome packaged in an icosahedral capsid of 180 copies of an identical protein (alpha protein). A fundamental property of many animal viruses is the post-assembly maturation required for infectivity. FHV is constructed as a provirion, which matures to an infectious virion by cleavage of alpha protein into beta and gamma subunits. We used high pressure, temperature and chemical denaturing agents to promote perturbation of the viral capsid. These effects were monitored by spectroscopy measurements (fluorescence, light scattering and CD) and size-exclusion chromatography. The data showed that FHV was stable to pressures up to 310 MPa at room temperature. The fluorescence emission and light scattering values showed small changes that were reversible after decompression. When we combined pressure and sub-denaturing urea concentrations (1 M), the changes were more drastic, suggesting dissociation of the capsid. However, these changes were reversible after pressure release. The complete dissociation of FHV could be observed only under high urea concentrations (10 M). There were no significant changes in emission spectra up to 5 M urea. FHV also was stable when we used temperature treatments (high and low). We also compared the effects of urea and pressure on FHV wild type and cleavage-defective mutant VLPs (virus-like particles). The VLPs and authentic particles are distinguishable by protein-RNA interactions, since VLPs pack cellular RNA and native particles contain viral RNA. Our results demonstrated that native particles are more stable than VLPs to physical and chemical treatments. Our data point to the specificity of the interaction between the capsid protein and the viral RNA. This specificity is crucial to the stability of the particle, which makes this interaction an excellent target for drug development.

Capsid↗
PubMed2003

Sediment microbes of deep-sea bioherms on the northwest shelf of Australia.

The northwest shelf of Australia is a region with known petroleum reserves. Recent geological investigations have revealed carbonate knolls postulated to be of biological origin. Sediment microbial populations at three sites on the northwest shelf, Pee Shoal, Mermaid Reef, and Scott Reef, were investigated for the presence of hydrocarbon-degrading bacteria. From two sampling trips, 246 bacterial strains were purified, and 182 of these strains displayed preferential growth on hydrocarbon-selective media. Strains were tested for nutrient specificity using single hydrocarbon fermentations. Metabolic profiles were constructed using biochemical testing, fatty acid analysis, and metabolic rate experiments. 16S rRNA gene sequence analysis of four strains identified these strains as members of the genera Sphingomonas, Bacillus, and Microbacterium, and one strain as a member of the alpha-Proteobacteria. The potential of these strains as bioindicators of hydrocarbon pollutants or for bioremediation in marine environments is discussed.

Australia↗
PubMed2003

Effects of the cowpea chlorotic mottle bromovirus beta-hexamer structure on virion assembly.

The X-ray crystal structure of Cowpea chlorotic mottle bromovirus (CCMV) revealed a unique tubular structure formed by the interaction of the N-termini from six coat protein subunits at each three-fold axis of the assembled virion. This structure, termed the beta-hexamer, consists of six short beta-strands. The beta-hexamer was postulated to play a critical role in the assembly and stability of the virion by stabilizing hexameric capsomers. Mutational analyses of the beta-hexamer structure, utilizing both in vitro and in vivo assembly assays, demonstrate that this structure is not required for virion formation devoid of nucleic acids in vitro or for RNA-containing virions in vivo. However, the beta-hexamer structure does contribute to virion stability in vitro and modulates disease expression in vivo. These results support a model for CCMV assembly through pentamer intermediates.

Base Sequence↗
PubMed2002

Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses.

A comparison of the recently determined structure of an insect picorna-like virus, Cricket paralysis virus (CrPV), with that of the mammalian picornaviruses shows that several structural features are highly conserved between these viruses. These conserved features include the topology of the coat proteins, the conformation of most loops, and the general arrangement of the internally located N-terminal arms of the coat proteins. The conformational conservation of the N-termini of the three major coat proteins between CrPV and the picornaviruses suggests a putative ancestral T = 3 virus. Comparisons of the genome structure and amino-acid sequence of the coat proteins of CrPV with a number of other insect picorna-like viruses show that most of them belong to a novel group, recently given the interim name Cricket paralysis-like viruses. Two other insect picorna-like viruses, Infectious flacherie virus (IFV) and Sacbrood virus (SBV), for which the genome sequences have recently been determined, have very different coat protein sequences and a genome organization more like the picornaviruses. However, the position of the small VP4 protein in the structural protein polyprotein as well as the mechanism for its cleavage from VP3 upon assembly strongly suggests an evolutionary link to the "Cricket paralysis-like viruses". We propose that the picornaviruses, Cricket paralysis-like viruses and IFV/SBV group are a natural assemblage. The ancestor for this assemblage had a structure based upon the CrPV/picornavirus paradigm and a genome encoding a single major coat protein; gene duplication and rearrangements have subsequently produced the viruses that we observe today. We also discuss the possible relatives of the proposed assemblage and the likely implications of future structural studies that may be carried out on the putative relatives.

Amino Acid Motifs↗
PubMed2002

Cowpea mosaic virus: from the presentation of antigenic peptides to the display of active biomaterials.

The potential of cowpea mosaic virus (CPMV), a plant icosahedral virus, for the presentation of foreign peptides and proteins is reported. The most prominent feature at the virus surface is a region of the smaller of the two coat proteins (S) which has been extensively used for the insertion of foreign peptides. Given the availability of the three-dimensional structure of the native virus and the amenability of foreign peptide-expressing CPMV chimeras to crystallisation, immunological data can be correlated with the conformational state of the foreign insert. The latter is influenced by proteolysis which occurs within the foreign inserts. In an effort to offer an alternative context for peptide expression, extensive exploration of a second region of the S protein is reported with respect to tolerance to small insertions. Moreover, to make CPMV suitable for a wider spectrum of presentation, a technique was developed to allow surface coupling of a peptide which can serve as the anchoring point for a range of proteins. This new approach is also widely applicable for the direct chemical cross-linking of peptides and full-length protein domains to the viral capsid.

Amino Acid Sequence↗
PubMed2001

Mechanisms of acid-catalyzed Z/E isomerization of imines.

The kinetics and mechanism of acid-catalyzed Z/E isomerization of O-methylbenzohydroximoyl chloride (1Za and 1Ea), methyl O-methylbenzohydroximate (1Zb and 1Eb), ethyl O-methylbenzohydroximate (1Zc and 1Ec and five para and meta substituted derivatives), O-methylcinnamohydroximoyl chloride (2Za and 2Ea), and methyl O-methylcinnamohydroximate (2Zb and 2Zb) have been investigated. The kinetics of Z/E isomerization of these imines have been studied in glacial acetic acid (1Ea and 1Zc) and in dioxane solutions containing HCl, trifluoromethanesulfonic acid, or tetrafluoroboric acid (1Ea, 1Zb, 2Ea, and 2Zb). The isomerization takes place by either (a) rotation about the carbon-nitrogen double bond of the protonated imine (iminium ion rotation) or (b) nucleophilic attack on the protonated imine to form a tetrahedral intermediate that undergoes stereomutation and loss of the nucleophile (nucleophilic catalysis). The hydroximoyl chlorides 1Eaand 2Ea only isomerize by the nucleophilic catalysis mechanism. The hydroximate 1Zb appears to be capable of isomerizing by either mechanism. The hydroximate 2Zb may be isomerizing only by iminium ion rotation. Theoretical calculations support the notion that increased conjugation in the protonated imine increases the rate of iminium ion rotation.

Acids↗
PubMed2001

Developmental changes in BDNF protein levels in the hamster retina and superior colliculus.

Quantitative studies of ontogenetic changes in the levels of brain-derived neurotrophic factor (BDNF) mRNA and its effector, BDNF protein, are not available for the retinal projection system. We used an electrochemiluminescence immunoassay to measure developmental changes in the tissue concentration of BDNF within the hamster retina and superior colliculus (SC). In the SC, we first detected BDNF (about 9 pg/mg tissue) on embryonic day 14 (E14). BDNF protein concentration in the SC rises about fourfold between (E14) and postnatal day 4 (P4), remains at a plateau through P15, then declines by about one-third to attain its adult level by P18. By contrast, BDNF protein concentration in the retina remains low (about 1 pg/mg tissue) through P12, then increases 4.5-fold to attain its adult level on P18. The developmental changes in retinal and collicular BDNF protein concentrations are temporally correlated with multiple events in the structural and functional maturation of the hamster retinal projection system. Our data suggest roles for BDNF in the cellular mechanisms underlying some of these events and are crucial to the design of experiments to examine those roles.

Animals↗
PubMed2001

Characterization of virus-like particles assembled in a recombinant baculovirus system expressing the capsid protein of a fish nodavirus.

Betanodaviruses are causative agents of neurological disorders in several species of fish. We cloned and sequenced the RNA2 segment of two grouper viruses isolated from Epinephelus malabaricus (malabaricus grouper nervous necrosis virus, MGNNV) and Epinephelus lanceolatus (dragon grouper nervous necrosis virus, DGNNV). The sequences of the two RNAs were 99% identical and comparison with previously sequenced RNA2 segments of fish nodaviruses striped jack nervous necrosis virus, Atlantic halibut virus, sea bass encephalitis virus, and greasy grouper nervous necrosis virus (GGNNV) revealed that MGNNV and DGNNV were most closely related to GGNNV. No correlation of sequence with geographical habitat was detected. The MGNNV coat protein, the gene product of RNA2, was expressed in Sf21 cells with a recombinant baculovirus system and virus-like particles (VLPs) spontaneously formed. Two types of VLPs were observed: a slower sedimenting particle was RNase-sensitive and stain-permeable, while the faster sedimenting particle survived RNase treatment and was not stain-permeable. An image reconstruction of the latter, obtained with electron cryomicroscopy data, revealed a morphology consistent with T = 3 quasi-symmetry but with features significantly different from insect nodavirus structures at the same resolution. This assembly system allows the first biophysical comparisons of fish and insect nodavirus structure, assembly, and stability.

Amino Acid Sequence↗
PubMed2001

Analysis of rapid, large-scale protein quaternary structural changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NomegaV) maturation.

Time-resolved small-angle X-ray scattering (TR-SAXS) was used to study the kinetics of a large conformational change that occurs during the maturation of an icosahedral virus. Virus-like particles (VLPs) of the T=4 non-enveloped RNA virus Nudaurelia capensis omega virus (NomegaV) were shown to undergo a large pH-dependent conformational change. Electron cryo-microscopy (cryoEM) and X-ray solution scattering were used to show that the precursor VLP (procapsid) was 16 % larger in diameter than the resulting capsid, which was shown by the cryoEM study to closely resemble the infectious mature virion. The procapsid form of the VLPs was observed at pH 7.5 and was converted to the capsid form at pH 5.0. Static SAXS measurements of the VLPs in solutions ranging between these pH values determined that the half-titration point of the transition was pH 6.0. Time-resolved SAXS experiments were performed on VLP solutions by initiating a pH change from 7.5 to 5.0 using a stopped-flow device, and the time-scale of the conformational change occurred in the subsecond range. Using a less drastic pH change (lowering the pH to 5.8 or 5.5), the conformational change occurred more slowly, on the subminute or minute time-scale, with the detection of a fast-forming intermediate in the transition. Further characterization using static SAXS measurements showed that the conformational change was initially reversible but became irreversible after autoproteolytic maturation was about 15 % complete. In addition to characterizing the large quaternary conformational change, we have been able for the first time to demonstrate that it takes place on the subsecond time-scale, a regime comparable to that observed in other multisubunit assemblies.

Capsid↗
PubMed2001

Characterization of an unknown component in Noscapine using liquid chromatography-mass spectrometry and proton nuclear magnetic resonance spectroscopy.

Analytical and semipreparative LC methods were used to quantitate and isolate an unknown component (Impurity A) found in samples of bulk Noscapine. This component was also examined by LC-ESI-MS and 1H-NMR. It was concluded that the structure of Impurity A only differed from Noscapine in that it possessed a hydroxyl group at position 21 of the isobenzofuranone moiety.

Chromatography, Liquid↗
PubMed2001

Crossinhibitory activities of Ngn1 and Math1 allow specification of distinct dorsal interneurons.

Distinct classes of neurons are generated from progenitor cells distributed in characteristic dorsoventral patterns in the developing spinal neural tube. We define restricted neural progenitor populations by the discrete, nonoverlapping expression of Ngn1, Math1, and Mash1. Crossinhibition between these bHLH factors is demonstrated and provides a mechanism for the generation of discrete bHLH expression domains. This precise control of bHLH factor expression is essential for proper neural development since as demonstrated in both loss- and gain-of-function experiments, expression of Math1 or Ngn1 in dorsal progenitor cells determines whether LH2A/B- or dorsal Lim1/2-expressing interneurons will develop. Together, the data suggest that although Math1 and Ngn1 appear to be redundant with respect to neurogenesis, they have distinct functions in specifying neuronal subtype in the dorsal neural tube.

Animals↗
PubMed2001

Effects of early visual experience and diurnal rhythms on BDNF mRNA and protein levels in the visual system, hippocampus, and cerebellum.

The expression of brain-derived neurotrophic factor (BDNF) mRNA and the secretion of BDNF protein are tightly regulated by neuronal activity. Thus, BDNF has been proposed as a mediator of activity-dependent neural plasticity. Previous studies showed that dark rearing (DR) reduces BDNF mRNA levels in the primary visual cortex (V1), but the effects of visual experience on BDNF protein levels are unknown. We report that rearing in constant light or DR alters BDNF mRNA and protein levels in the retina, superior colliculus (SC), V1, hippocampus (HIPP), and cerebellum (CBL), although the changes in mRNA and protein are not always correlated. Most notably, DR increases BDNF protein levels in V1 although BDNF mRNA is decreased. BDNF protein levels also undergo diurnal changes. In the retina, V1, and SC, BDNF protein levels are higher during the light phase of the circadian cycle than during the dark phase. By contrast, in HIPP and CBL, the tissue concentration of BDNF protein is higher during the dark phase. The discrepancies between the experience-dependent changes in BDNF mRNA and protein suggest that via its effects on neuronal activity, early sensory experience alters the trafficking, as well as the synthesis, of BDNF protein. The circadian changes in BDNF protein suggest that BDNF could cause the diurnal modulation of synaptic efficacy in some neural circuits. The fluctuations in BDNF levels in nonvisual structures suggest a potential role of BDNF in mediating plasticity induced by hormones or motor activity.

Aging↗