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Biomedical subjects

J E Johnson

Publications and source records attributed to J E Johnson.

At least 73 records · Page 4Linked to original sources
PubMed2000

PANAL: an integrated resource for Protein sequence ANALysis.

SUMMARY: We present PANAL, an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the result as an intuitive graphical summary.

Computational Biology↗
PubMed2000

Increased resolution data from a large unit cell crystal collected at a third-generation synchrotron X-ray source.

A third-generation synchrotron source was used to collect data from crystals with a very large unit cell. There was an increase in the effective resolution of the data from 5 to 3.5 A. Data were collected on crystals of HK97 mature empty capsids, space group P2(1), with unit-cell parameters a = 580, b = 625, c = 790 A, beta = 90.0 degrees. Like other crystals with very large unit-cell dimensions, the intensity falls off rapidly as a function of resolution, with a precipitous drop beginning at 9 A resolution. Synchrotron data from these crystals were previously observed at the CHESS F1 beamline to about 3.5 A resolution, but the intensities could not be accurately measured beyond 5 A. In experiments conducted at the Advanced Photon Source (APS) beamline 14-BM-C, data from identical crystals could be processed to a resolution of 3.5 A. The lifetime of the crystals in the beam was increased from one exposure per crystal volume to between four and eight exposures per crystal volume. More than 500 images were collected in two trips, allowing the extension of the resolution of the data set and the structure determination to 3.5 A resolution. Factors in the increased resolution may include X-ray flux, beamline geometry and low background scatter. These results suggest that other crystals with large unit cells and pronounced intensity falloff with resolution may benefit from the use of this or similar beamlines.

Capsid↗
PubMed2000

Structural fingerprinting: subgrouping of comoviruses by structural studies of red clover mottle virus to 2.4-A resolution and comparisons with other comoviruses.

Red clover mottle virus (RCMV) is a member of the comoviruses, a group of picornavirus-like plant viruses. The X-ray structure of RCMV strain S has been determined and refined to 2.4 A. The overall structure of RCMV is similar to that of two other comoviruses, Cowpea mosaic virus (CPMV) and Bean pod mottle virus (BPMV). The sequence of the coat proteins of RCMV strain O were modeled into the capsid structure of strain S without causing any distortion, confirming the close resemblance between the two strains. By comparing the RCMV structure with that of other comoviruses, a structural fingerprint at the N terminus of the small subunit was identified which allowed subgrouping of comoviruses into CPMV-like and BPMV-like viruses.

Amino Acid Sequence↗
PubMed2000

Rescue of mumps virus from cDNA.

A complete DNA copy of the genome of a Jeryl Lynn strain of mumps virus (15,384 nucleotides) was assembled from cDNA fragments such that an exact antigenome RNA could be generated following transcription by T7 RNA polymerase and cleavage by hepatitis delta virus ribozyme. The plasmid containing the genome sequence, together with support plasmids which express mumps virus NP, P, and L proteins under control of the T7 RNA polymerase promoter, were transfected into A549 cells previously infected with recombinant vaccinia virus (MVA-T7) that expressed T7 RNA polymerase. Rescue of infectious virus from the genome cDNA was demonstrated by amplification of mumps virus from transfected-cell cultures and by subsequent consensus sequencing of reverse transcription-PCR products generated from infected-cell RNA to verify the presence of specific nucleotide tags introduced into the genome cDNA clone. The only coding change (position 8502, A to G) in the cDNA clone relative to the consensus sequence of the Jeryl Lynn plaque isolate from which it was derived, resulting in a lysine-to-arginine substitution at amino acid 22 of the L protein, did not prevent rescue of mumps virus, even though an amino acid alignment for the L proteins of paramyxoviruses indicates that lysine is highly conserved at that position. This system may provide the basis of a safe and effective virus vector for the in vivo expression of immunologically and biologically active proteins, peptides, and RNAs.

Animals↗
PubMed2000

Subtalar arthrodesis with flexor digitorum longus transfer and spring ligament repair for treatment of posterior tibial tendon insufficiency.

The surgical treatment of flexible pes planovalgus deformities resulting from Stage 2 posterior tibial tendon insufficiency is controversial and many techniques have been proposed. We retrospectively reviewed the results of subtalar arthrodesis combined with spring ligament repair/reefing and flexor digitorum longus (FDL) transfer to the navicular. There were sixteen patients (seventeen feet) with an average follow-up of 27 months (9-52). All deformities were passively correctable. The average age was 56 yrs (39-78). All patients had failed conservative management, 88% had previously been treated with orthotics, and 53% had lateral pain from subfibular impingement. Two patients were noted to have degenerative changes of the subtalar joint. Successful subtalar joint fusion occurred in all patients with an average time to radiographic union of 10.1 weeks (5-24). The average AOFAS hindfoot score and Maryland foot score postoperatively was 82 and 86 respectively. Standing radiographic analysis demonstrated an average improvement in the AP talo-1st metatarsal angle of 6 degrees (24 degrees preoperative, 18 degrees postoperative). The talonavicular coverage angle improved an average of 17 degrees (34 degrees preoperative, 17 degrees postoperative). The lateral talo-1st metatarsal angle improved an average of 10 degrees (18 degrees preoperative, 8 degrees postoperative). The lateral talocalcaneal angle decreased an average of 21o (55 degrees preoperative, 34 degrees postoperative). The distance of the medial cuneiform to the floor on the lateral radiograph averaged 12mm preoperatively and 18mm postoperatively (avg. improvement 6mm). The combination of the flexor digitorum longus tendon transfer and spring ligament repair with subtalar arthrodesis is an effective and reliable procedure which provides excellent correction of hindfoot valgus as well as forefoot abduction and restoration of the height of the longitudinal arch. These results compare favorably with flexor transfer combined with either calcaneal osteotomy or lateral column lengthening.

Adult↗
PubMed2000

Assessment of older urban drivers by nurse practitioners.

Thirty-five older urban adults who had forfeited a driver's license and 25 nurse practitioners (NPs) who provided health care to them participated in a qualitative study to (a) explore the perception of NPs regarding their role in assessing the driving abilities of older adults, (b) describe the ways in which NPs assist their clients to cope with the loss of a driver's license, and (c) delineate the NPs influence on the elders' decision to forfeit their license. Findings suggest that most NPs had concerns about their older clients' driving abilities. However, assessment of parameters related to driving safety was not their primary objective. An NPs recommendation to forfeit a license was important to the older driver's decision to do so. Assisting clients with the consequences of no longer driving was difficult for a variety of reasons.

Adult↗
PubMed2000

Autoregulation and multiple enhancers control Math1 expression in the developing nervous system.

Development of the vertebrate nervous system requires the actions of transcription factors that establish regional domains of gene expression, which results in the generation of diverse neuronal cell types. MATH1, a transcription factor of the bHLH class, is expressed during development of the nervous system in multiple neuronal domains, including the dorsal neural tube, the EGL of the cerebellum and the hair cells of the vestibular and auditory systems. MATH1 is essential for proper development of the granular layer of the cerebellum and the hair cells of the cochlear and vestibular systems, as shown in mice carrying a targeted disruption of Math1. Previously, we showed that 21 kb of sequence flanking the Math1-coding region is sufficient for Math1 expression in transgenic mice. Here we identify two discrete sequences within the 21 kb region that are conserved between mouse and human, and are sufficient for driving a lacZ reporter gene in these domains of Math1 expression in transgenic mice. The two identified enhancers, while dissimilar in sequence, appear to have redundant activities in the different Math1 expression domains except the spinal neural tube. The regulatory mechanisms for each of the diverse Math1 expression domains are tightly linked, as separable regulatory elements for any given domain of Math1 expression were not found, suggesting that a common regulatory mechanism controls these apparently unrelated domains of expression. In addition, we demonstrate a role for autoregulation in controlling the activity of the Math1 enhancer, through an essential E-box consensus binding site.

Animals↗
PubMed2000

Posterior tibial tendon dysfunction.

Posterior tibial tendon dysfunction is the most common cause of acquired flatfoot deformity in adults. Although this term suggests pathology involving only the posterior tibial tendon, the disorder includes a spectrum of pathologic changes involving associated tendon, ligament, and joint structures of the ankle, hindfoot, and midfoot. Early recognition and treatment is the key to prevention of the debilitating, long-term consequences of this disorder. Conservative care is possible in the earliest stages, whereas surgical reconstruction and eventually arthrodeses become necessary in the latter stages. The purpose of this article is to review the symptoms, physical examination, radiological examination, classification, and treatment of posterior tibial tendon dysfunction.

Arthrodesis↗
PubMed2000

Effects of a tendo-Achilles lengthening procedure on muscle function and gait characteristics in a patient with diabetes mellitus.

STUDY DESIGN: Case report with repeated measures. OBJECTIVES: To describe the effects of a tendo-Achilles lengthening (TAL) and total contact casting (TCC) on wound healing, motion, plantar pressure, and function in a patient with diabetes mellitus, peripheral neuropathy, neuropathic ulcer, and limited dorsiflexion range of motion (DFROM). BACKGROUND: Limited DFROM has been associated with increased forefoot pressures and skin breakdown. A TAL was expected to increase DFROM and reduce forefoot pressures during walking, but the influence on muscle performance and function was unknown. METHODS AND MEASURES: The patient was a 42-year-old man with a 20-year history of type 1 diabetes (NIDDM) and a recurrent neuropathic plantar ulcer. Outcome measures were DFROM, isokinetic plantar flexor muscle peak torque, in-shoe and barefoot peak plantar pressure, physical performance test (PPT) score, and peak ankle and hip moments during walking obtained from an automated gait analysis. All tests were completed pre-TAL, 8 weeks post-TAL (after immobilization in a TCC), and 7 months post-TAL. RESULTS: The wound healed in 40 days. The TAL resulted in a sustained increase in DFROM (0 to 18 degrees). Plantar flexor peak torque was reduced by 21% 8 weeks after the TAL compared with the torque before surgery but recovered fully at 7 months. Seven months following TAL, in-shoe forefoot peak plantar pressure was reduced by 55%, barefoot pressure decreased by 14%, PPT score increased by 24%, peak ankle plantar flexor moment remained decreased by 30%, and the peak hip flexor moment increased by 41% during walking. CONCLUSION: For this patient, a TAL resulted in short-term deficits in peak plantar flexor torque, but a 7-month follow-up showed improvements in ankle DFROM, walking ability, and a decrease in forefoot in-shoe peak plantar pressure.

Achilles Tendon↗
PubMed1999

Graded and areal expression patterns of regulatory genes and cadherins in embryonic neocortex independent of thalamocortical input.

The differentiation of areas of the mammalian neocortex has been hypothesized to be controlled by intrinsic genetic programs and extrinsic influences such as those mediated by thalamocortical afferents (TCAs). To address the interplay between these intrinsic and extrinsic mechanisms in the process of arealization, we have analyzed the requirement of TCAs in establishing or maintaining graded or areal patterns of gene expression in the developing mouse neocortex. We describe the differential expression of Lhx2, SCIP, and Emx1, representatives of three different classes of transcription factors, and the type II classical cadherins Cad6, Cad8, and Cad11, which are expressed in graded or areal patterns, as well as layer-specific patterns, in the cortical plate. The differential expression of Lhx2, SCIP, Emx1, and Cad8 in the cortical plate is not evident until after TCAs reach the cortex, whereas Cad6 and Cad11 show subtle graded patterns of expression before the arrival of TCAs, which later become stronger. We find that these genes exhibit normal-appearing graded or areal expression patterns in Mash-1 mutant mice that fail to develop a TCA projection. These findings show that TCAs are not required for the establishment or maintenance of the graded and areal expression patterns of these genes and strongly suggest that their regulation is intrinsic to the developing neocortex.

Animals↗
PubMed1999

The refined crystal structure of cowpea mosaic virus at 2.8 A resolution.

Comoviruses are a group of plant viruses in the picornavirus superfamily. The type member of comoviruses, cowpea mosaic virus (CPMV), was crystallized in the cubic space group I23, a = 317 A and the hexagonal space group P6(1)22, a = 451 A, c = 1038 A. Structures of three closely similar nucleoprotein particles were determined in the cubic form. The roughly 300-A capsid was similar to the picornavirus capsid displaying a pseudo T = 3 (P = 3) surface lattice. The three beta-sandwich domains adopt two orientations, one with the long axis radial and the other two with the long axes tangential in reference to the capsid sphere. T = 3 viruses display one or the other of these two orientations. The CPMV capsid was permeable to cesium ions, leading to a disturbance of the beta-annulus inside a channel-like structure, suggesting an ion channel. The hexagonal crystal form diffracted X rays to 3 A resolution, despite the large unit cell. The large ( approximately 200 A) solvent channels in the lattice allow exchange of CPMV cognate Fab fragments. As an initial step in the structure determination of the CPMV/Fab complex, the P6(1)22 crystal structure was solved by molecular replacement with the CPMV model determined in the cubic cell.

Amino Acid Sequence↗
PubMed1999

RNA-controlled polymorphism in the in vivo assembly of 180-subunit and 120-subunit virions from a single capsid protein.

Repeated, specific interactions between capsid protein (CP) subunits direct virus capsid assembly and exemplify regulated protein-protein interactions. The results presented here reveal a striking in vivo switch in CP assembly. Using cryoelectron microscopy, three-dimensional image reconstruction, and molecular modeling, we show that brome mosaic virus (BMV) CP can assemble in vivo two remarkably distinct capsids that selectively package BMV-derived RNAs in the absence of BMV RNA replication: a 180-subunit capsid indistinguishable from virions produced in natural infections and a previously unobserved BMV capsid type with 120 subunits arranged as 60 CP dimers. Each such dimer contains two CPs in distinct, nonequivalent environments, in contrast to the quasi-equivalent CP environments throughout the 180-subunit capsid. This 120-subunit capsid utilizes most of the CP interactions of the 180-subunit capsid plus nonequivalent CP-CP interactions. Thus, the CP of BMV, and perhaps other viruses, can encode CP-CP interactions that are not apparent from mature virions and may function in assembly or disassembly. Shared structural features suggest that the 120- and 180-subunit capsids share assembly steps and that a common pentamer of CP dimers may be an important assembly intermediate. The ability of a single CP to switch between distinct capsids by means of alternate interactions also implies reduced evolutionary barriers between different capsid structures. The in vivo switch between alternate BMV capsids is controlled by the RNA packaged: a natural BMV genomic RNA was packaged in 180-subunit capsids, whereas an engineered mRNA containing only the BMV CP gene was packaged in 120-subunit capsids. RNA features can thus direct the assembly of a ribonucleoprotein complex between alternate structural pathways.

Bromovirus↗
PubMed1999

Preferential role for NF-kappa B/Rel signaling in the type 1 but not type 2 T cell-dependent immune response in vivo.

T cell function is a critical determinant of immune responses as well as susceptibility to allergic diseases. Activated T cells can differentiate into effectors whose cytokine profile is limited to type 1 (IFN-gamma-dominant) or type 2 (IL-4-, IL-5-dominant) patterns. To investigate mechanisms that connect extracellular stimuli with the regulation of effector T cell function, we have measured immune responses of transgenic mice whose NF-kappa B/Rel signaling pathway is inhibited in T cells. Surprisingly, these mice developed type 2 T cell-dependent responses (IgE and eosinophil recruitment) in a model of allergic pulmonary inflammation. In contrast, type 1 T cell responses were severely impaired, as evidenced by markedly diminished delayed-type hypersensitivity responses, IFN-gamma production, and Ag-specific IgG2a levels. Taken together, these data indicate that inhibition of NF-kappa B can lead to preferential impairment of type 1 as compared with type 2 T cell-dependent responses.

Animals↗