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Biomedical subjects

J E Johnson

Publications and source records attributed to J E Johnson.

At least 37 records · Page 2Linked to original sources
PubMed2001

Target-derived BDNF (brain-derived neurotrophic factor) is essential for the survival of developing neurons in the isthmo-optic nucleus.

Neurons in the peripheral nervous system depend on single neurotrophic factors, whereas those in the brain are thought to utilize many different trophic factors. This study examined whether some neurons in the brain critically depend on a single trophic factor during development. Neurons in the isthmo-optic nucleus (ION) of chick embryos respond to exogenous brain-derived neurotrophic factor (BDNF). Relatively high concentrations of endogenous BDNF were present in the ION of 14-18-day-old chick embryos. ION target cells in the retina were immunolabeled for BDNF but showed surprisingly low levels of BDNF mRNA. These data suggest that ION target cells derive some BDNF from other retinal sources. No BDNF mRNA was detected in the ION itself. ION neurons had a very efficient retrograde transport system for BDNF and exogenous BDNF arrived in the ION intact. When the ION was deprived of endogenous trkB ligands by injection of trkB fusion proteins in the eye, cell death of ION neurons was enhanced, and this effect was mimicked by BDNF-specific blocking antibodies in the eye. TrkB fusion proteins in the retina induced cell death of ION neurons prior to visible effects on ION target cells in the retina. Immunolabel for endogenous BDNF was sparse in pyknotic ION neurons, suggesting that ION neurons with low BDNF content were eliminated by apoptosis. These data show that BDNF is an essential target-derived trophic factor for developing ION neurons and thereby validate the neurotrophic hypothesis for at least one neuronal population in the brain.

Animals↗
PubMed2001

Virus maturation involving large subunit rotations and local refolding.

Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a catenated cross-linked topology. We have visualized its precursor, Prohead-II, by cryoelectron microscopy and modeled the conformational change by appropriately adapting Head-II. Rigid-body rotations ( approximately 40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially approximately 40 angstroms apart, close together. The inner surface of Prohead-II is negatively charged, suggesting that the transition is triggered electrostatically by DNA packaging.

Amino Acid Motifs↗
PubMed2001

Viral capsid mobility: a dynamic conduit for inactivation.

Mass spectrometry and fluorescent probes have provided direct evidence that alkylating agents permeate the protein capsid of naked viruses and chemically inactivate the nucleic acid. N-acetyl-aziridine and a fluorescent alkylating agent, dansyl sulfonate aziridine, inactivated three different viruses, flock house virus, human rhinovirus-14, and foot and mouth disease virus. Mass spectral studies as well as fluorescent probes showed that alkylation of the genome was the mechanism of inactivation. Because particle integrity was not affected by selective alkylation (as shown by electron microscopy and sucrose gradient experiments), it was reasoned that the dynamic nature of the viral capsid acts as a conduit to the interior of the particle. Potential applications include fluorescent labeling for imaging viral genomes in living cells, the sterilization of blood products, vaccine development, and viral inactivation in vivo.

Animals↗
PubMed2001

Neurogenin2 expression in ventral and dorsal spinal neural tube progenitor cells is regulated by distinct enhancers.

The basic helix-loop-helix transcription factor Neurogenin2 (NGN2) is expressed in distinct populations of neural progenitor cells within the developing central and peripheral nervous systems. Transgenic mice containing ngn2/lacZ reporter constructs were used to study the regulation of ngn2 in the developing spinal cord. ngn2/lacZ transgenic embryos containing sequence found 5' or 3' to the ngn2 coding region express lacZ in domains that reflect the spatial and temporal expression profile of endogenous ngn2. A 4.4-kb fragment 5' of ngn2 was sufficient to drive lacZ expression in the ventral neural tube, whereas a 1.0-kb fragment located 3' of ngn2 directed expression to both dorsal and ventral domains. Persistent -gal activity revealed that the NGN2 progenitor cells in the dorsal domain give rise to a subset of interneurons that send their axons to the floor plate, and the NGN2 progenitors in the ventral domain give rise to a subset of motor neurons. We identified a discrete element that is required for the activity of the ngn2 enhancer specifically in the ventral neural tube. Thus, separable regulatory elements that direct ngn2 expression to distinct neural progenitor populations have been defined.

Animals↗
PubMed2001

The MetaFam Server: a comprehensive protein family resource.

MetaFam is a comprehensive relational database of protein family information. This web-accessible resource integrates data from several primary sequence and secondary protein family databases. By pooling together the information from these disparate sources, MetaFam is able to provide the most complete protein family sets available. Users are able to explore the interrelationships among these primary and secondary databases using a powerful graphical visualization tool, MetaFamView. Additionally, users can identify corresponding sequence entries among the sequence databases, obtain a quick summary of corresponding families (and their sequence members) among the family databases, and even attempt to classify their own unassigned sequences. Hypertext links to the appropriate source databases are provided at every level of navigation. Global family database statistics and information are also provided. Public access to the data is available at http://metafam.ahc.umn.edu/.

Computational Biology↗
PubMed2001

Purification, crystallization, and preliminary X-ray analysis of L-A: a dsRNA yeast virus.

TheL-A virus (LAV) particle is a specialized compartment for the transcription and replication of double-stranded RNA. It is 390 A in diameter and infects yeast. The particle is formed by a capsid containing 120 copies of a 680-residue gene product arranged with T = 1 icosahedral symmetry, approximately two copies of an RNA-directed RNA polymerase, and a 4.6-kb linear, duplex RNA. LAV crystals diffracting to at least 4.5-A resolution were grown in a combination of polyethylene glycol 8000, ethylene glycol, and lithium chloride. Following crystallization the reservoir solution was replaced by a 2x concentrated reservoir solution in order for ethylene glycol to function as a cryoprotectant even though initial crystals would not grow at sufficiently high concentrations of ethylene glycol for cryoprotection. A complete data set was collected to 6-A resolution from a frozen crystal obtained with this procedure. The crystals belong to space group P2(1). The unit cell dimensions are a = 406.7 A, b = 403.3 A, c = 572.5 A, beta = 90.3 degrees with two virus particles in the unit cell. The particle orientation was determined with the rotation function and the particle center was estimated on the basis of packing considerations.

Capsid↗
PubMed2001

Overexpression of MATH1 disrupts the coordination of neural differentiation in cerebellum development.

An essential role for the bHLH transcription factor MATH1 in the formation of cerebellar granule cells was previously demonstrated in a Math1 null mouse. The function of regulated levels of MATH1 in granule cell development is investigated here using a gain-of-function paradigm. Overexpression of Math1 in its normal domain in transgenic mice leads to early postnatal lethality and perturbs cerebellar development. The cerebellum of the (B)MATH1 transgenic neonate is smaller with less foliation, particularly in the central vermal regions, when compared to wild-type cerebella. A detailed analysis of multiple molecular markers in brains overexpressing Math1 has revealed defects in the differentiation of cerebellar granule cells. NeuroD and doublecortin, markers normally distinguishing the discrete layered organization of granule cell maturation in the inner EGL, are aberrantly expressed in the outer EGL where MATH1-positive, proliferating cells reside. In contrast, TAG-1, a later marker of developing granule cells that labels parallel fibers, is severely diminished. The elevated MATH1 levels appear to drive expression of a subset of early differentiation markers but are insufficient for development of a mature TAG-1-expressing granule cell. Thus, balanced levels of MATH1 are essential for the correct coordination of differentiation events in granule cell development.

Animals↗
PubMed2001

Effects of paramyxoviral infection on airway epithelial cell Foxj1 expression, ciliogenesis, and mucociliary function.

To elucidate molecular mechanisms underlying the association between respiratory viral infection and predisposition to subsequent bacterial infection, we used in vivo and in vitro models and human samples to characterize respiratory virus-induced changes in airway epithelial cell morphology, gene expression, and mucociliary function. Mouse paramyxoviral bronchitis resulted in airway epithelial cell infection and a distinct pattern of epithelial cell morphology changes and altered expression of the differentiation markers beta-tubulin-IV, Clara cell secretory protein, and Foxj1. Furthermore, changes in gene expression were recapitulated using an in vitro epithelial cell culture system and progressed independent of the host inflammatory response. Restoration of mature airway epithelium occurred in a pattern similar to epithelial cell differentiation and ciliogenesis in embryonic lung development characterized by sequential proliferation of undifferentiated cells, basal body production, Foxj1 expression, and beta-tubulin-IV expression. The effects of virus-induced alterations in morphology and gene expression on epithelial cell function were illustrated by decreased airway mucociliary velocity and impaired bacterial clearance. Similar changes in epithelial cell Foxj1 expression were also observed in human paramyxoviral respiratory infection. Taken together, these model systems of paramyxoviral respiratory infection mimic human pathology and identify epithelial cell Foxj1 expression as an early marker of epithelial cell differentiation, recovery, and function.

Animals↗
PubMed2001

Calculus formation on a retained Acucise wire.

We report the case of a patient who developed an obstructing calculus embedded at the ureteropelvic junction after treatment of ureteropelvic junction obstruction with the Acucise cutting balloon catheter. Within the length of the stone, we found a wire consistent with the cutting wire. To our knowledge, this is the first report of a fractured and retained cutting wire resulting in calculus formation.

Adult↗
PubMed2001

A role for the helix-loop-helix protein Id2 in the control of oligodendrocyte development.

Compared to neurons, the intracellular mechanisms that control glial differentiation are still poorly understood. We show here that oligodendrocyte lineage cells express the helix-loop-helix proteins Mash1 and Id2. Although Mash1 has been found to regulate neuronal development, we found that in the absence of Mash1 oligodendrocyte differentiation occurs normally. In contrast, we found that overexpression of Id2 powerfully inhibits oligodendrocyte differentiation, that Id2 normally translocates out of the nucleus at the onset of differentiation, and that absence of Id2 induces premature oligodendrocyte differentiation in vitro. These findings demonstrate that Id2 is a component of the intracellular mechanism that times oligodendrocyte differentiation and point to the existence of an as yet unidentified MyoD-like bHLH protein necessary for oligodendrocyte differentiation.

Animals↗
PubMed2001

Subtalar arthrodesis for treatment of posterior tibial tendon insufficiency.

Subtalar arthrodesis is an effective treatment of the planovalgus deformity of posterior tibial tendon insufficiency that provides stable and reliable results with minimal complications. Disadvantages include the risk of symptomatic adjacent joint arthrosis at long-term follow-up and less clinical and radiographic correction of the deformity as compared with other reconstructive options, which may make the joint-preserving procedures more attractive for the primary treatment of patients with a flexible pes planovalgus deformity without subtalar pain.

Arthrodesis↗
PubMed2001

The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA.

The 3.0 A resolution crystal structure of Pariacoto virus (PaV) reveals extensive interactions between portions of the viral RNA genome and the icosahedral capsid. Under the protein shell of the T = 3 quasi equivalent capsid lies a dodecahedral cage composed of RNA duplex that accounts for approximately 35% of the single-stranded RNA genome. The highly basic N-terminal regions (residues 7-54) of the subunits, forming pentamers (A subunits) are clearly visible in the density map and make numerous interactions with the RNA cage. The C-terminal segments (residues 394-401) of the A subunits lie in channels near the quasi three-fold axes. Electron cryo-microscopy and image reconstruction of PaV particles clearly show the dodecahedral RNA cage.

Amino Acid Sequence↗
PubMed2001

Comparing transforming growth factor beta-2 and fibronectin as pleurodesing agents.

BACKGROUND: We have recently demonstrated that transforming growth factor beta-2 (TGF-beta2) can produce effective pleurodesis. Whether this effect can be reproduced by the use of its downstream proteins is not known. This study compared the effectiveness of TGF-beta2 and fibronectin in inducing pleurodesis in rabbits. METHODOLOGY: New Zealand white rabbits (1.5-2.0 kg) were given 1.7 microg of TGF-beta2 (n=5) or 2.0 mg of cellular fibronectin (n=4) intrapleurally via a chest tube. The induced pleural fluid was collected and analyzed. The rabbits were sacrificed after 14 days. The pleurodesis was graded macroscopically from 1 (none) to 8 (symphysis > 50%). RESULTS: All rabbits in the TGF-beta2 group developed effective pleurodesis while none in the fibronectin group had scores > 2 (pleurodesis scores 7.0 +/- 0.6 vs 1.3 +/- 0.3, P < 0.001). Rabbits that received TGF-beta2 produced large amounts of pleural fluid initially (< 4 days). Microscopically, the pleura of rabbits in the TGF-beta2 group showed prominent spindle cell proliferation and collagen deposition, but no significant inflammation or mesothelial proliferation. Pleural tissues of rabbits in the fibronectin group had occasional thin collagen deposits only. The intrapleural administration of 2.0 mg of fibronectin, a downstream product of TGF-beta, did not induce effective pleurodesis, as did the intrapleural administration of TGF-beta2. CONCLUSIONS: The present study suggests that the mechanism by which TGF-beta2 induces pleurodesis is not predominantly dependent on the production of fibronectin.

Animals↗
PubMed2001

Obstructive jaundice secondary to lymphoma in childhood.

In children, biliary obstruction secondary to lymphoma is rare. Previous reports in adults and children suggest that these lymphomas are associated with a poor prognosis. The authors reviewed the medical records and imaging studies of 4 children treated for pancreaticobiliary lymphoma at our children's hospital over the past 10 years. All 4 presented with jaundice. Abdominal ultrasound scan and computed tomography (CT) scans were helpful in defining the anatomy of the obstruction. In the cases of involvement of the porta hepatis, the diagnosis was made by biopsy. In one child a mass was in the head of the pancreas, and evaluation of frozen section biopsy results were not diagnostic for lymphoma, and a major resection was performed. All the lymphomas were of nonHodgkin's B-cell type and one was a Burkitt's lymphoma. All responded promptly to chemotherapy. One child had a testicular relapse and currently is receiving additional therapy. Pancreaticobiliary lymphomas are an unusual cause of obstructive jaundice in children. Biopsy alone without resection or biliary drainage is recommended surgical therapy. Long-term survival rate in children with this disorder appears to be more promising than previously reported. J Pediatr Surg 36:1792-1795.

Antineoplastic Agents↗
PubMed2001

MetaFam: a unified classification of protein families. I. Overview and statistics.

MOTIVATION: Protein sequence classification is becoming an increasingly important means of organizing the voluminous data produced by large-scale genome sequencing projects. At present, there are several independent classification methods. To aid the general classification effort, we have created a unified protein family resource, MetaFam. MetaFam is a protein family classification built upon 10 publicly-accessible protein family databases (Blocks + DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE, and SYSTERS). MetaFam's family 'supersets', as we call them, are created automatically using set-theory to compare families among the databases. Families of one database are matched to those in another when the intersection of their members exceeds all other possible family pairings between the two databases. Pairwise family matches are drawn together transitively to create a new list of protein family supersets. RESULTS: MetaFam family supersets have several useful features: (1) each superset contains more members than the families from which it is composed, because each of the component family databases only works with a subset of our full non-redundant set of proteins; (2) conflicting assignments can be pinpointed quickly, since our analysis identifies individual members that are in conflict with the majority consensus; (3) family descriptions that are absent from automated databases can frequently be assigned; (4) statistics have been computed comparing domain boundaries, family size distributions, and overall quality of MetaFam supersets; (5) the supersets have been loaded into a relational database to allow for complex queries and visualization of the connections among families in a superset and the consensus of individual domain members; and (6) the quality of individual supersets has been assessed using numerous quantitative measures such as family consistency, connectedness, and size. We anticipate this new resource will be particularly useful to genomic database curators.

Data Interpretation, Statistical↗
PubMed2001

MetaFam: a unified classification of protein families. II. Schema and query capabilities.

MOTIVATION: Protein sequence and family data is accumulating at such a rapid rate that state-of-the-art databases and interface tools are required to aid curators with their classifications. We have designed such a system, MetaFam, to facilitate the comparison and integration of public protein sequence and family data. This paper presents the global schema, integration issues, and query capabilities of MetaFam. RESULTS: MetaFam is an integrated data warehouse of information about protein families and their sequences. This data has been collected into a consistent global schema, and stored in an Oracle relational database. The warehouse implementation allows for quick removal of outdated data sets. In addition to the relational implementation of the primary schema, we have developed several derived tables that enable efficient access from data visualization and exploration tools. Through a series of straightforward SQL queries, we demonstrate the usefulness of this data warehouse for comparing protein family classifications and for functional assignment of new sequences.

Databases, Factual↗