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Biomedical subjects

P Bourne

Publications and source records attributed to P Bourne.

12 recordsLinked to original sources
PubMed2000

Expression of mPer1 and mPer2, two mammalian clock genes, in murine bone marrow.

Although circadian variations in hematopoiesis have been well documented, the molecular mechanism of the circadian rhythms remains elusive. To determine if a clock system exists in bone marrow to mediate the circadian rhythms, we analyzed the expression of mPer1 and mPer2, both mouse homologues of the Drosophila period gene and known regulators of the clock system, in murine bone marrow by relative quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). We demonstrated that both genes were expressed in bone marrow. Furthermore, the expression patterns of mPer1 and mPer2 in total bone marrow cells exhibited two peaks over a 24-h period. In contrast, the expression patterns of these two genes in the Gr-1-positive cells isolated from bone marrow mainly contributed to one of the two peaks. These results indicate that a clock system exists in bone marrow and suggest that the circadian rhythms in bone marrow are lineage- and/or differentiation stage-dependent.

Analysis of Variance↗
PubMed1999

Phytoecdysteroids in seeds and plants of Rhagodia baccata (Labill.) Moq. (Chenopodiaceae).

Seeds of Rhagodia baccata afforded, in addition to 20-hydroxy-ecdysone and polypodine B, a novel phytoecdysteroid, (20R)-22-deoxy-20,21-dihydroxyecdysone, the structure of which was elucidated unequivocally by UV, LSIMS and NMR techniques. This compound possessed agonistic activity in the Drosophila melanogaster BII cell bioassay, with an ED50 value of 2.0 x 10(-7)M (ED50 value for 20-hydroxyecdysone = 7.5 x 10(-9)M). The distribution of ecdysteroids in plants of R. baccata has been determined. Highest levels are associated with the youngest aerial tissues and with the roots. Ecdysteroid profiles are qualitatively very similar throughout the plant, with 20-hydroxyecdysone and polypodine B predominating in all plant parts tested.

Animals↗
PubMed1999

PGP9.5: a marker for cellular neurothekeoma.

Neurothekeomas are benign, predominantly cutaneous neoplasms that are divided histologically into myxoid, intermediate, and cellular types. Although it is generally agreed that the myxoid type of neurothekeoma has a neural origin, the lack of consistent immunoreactivity to neural markers and insufficient ultrastructural evidence of neural differentiation in cellular neurothekeoma have brought the origin of cellular neurothekeoma into question. In this report the authors show that immunoreactivity to protein gene product 9.5 (PGP9.5)--a broad neural marker--is positive in 100% of cases of cellular neurothekeoma using microwave antigen retrieval, as well as in all cases of myxoid and intermediate neurothekeoma. In contrast, immunoreactivity to S-100 protein is only positive in 3 of 12 cases of cellular neurothekeoma. These results show that PGP9.5 is a useful marker for identifying cellular neurothekeoma, as well as other types of neurothekeomas using the antigen retrieval method. The results are consistent with the notion that cellular neurothekeoma has a neural differentiation.

Adolescent↗
PubMed1998

A prototype molecular interactive collaborative environment (MICE).

Illustrations of macromolecular structure in the scientific literature contain a high level of semantic content through which the authors convey, among other features, the biological function of that macromolecule. We refer to these illustrations as molecular scenes. Such scenes, if available electronically, are not readily accessible for further interactive interrogation. The basic PDB format does not retain features of the scene; formats like PostScript retain the scene but are not interactive; and the many formats used by individual graphics programs, while capable of reproducing the scene, are neither interchangeable nor can they be stored in a database and queried for features of the scene. MICE defines a Molecular Scene Description Language (MSDL) which allows scenes to be stored in a relational database (a molecular scene gallery) and queried. Scenes retrieved from the gallery are rendered in Virtual Reality Modeling Language (VRML) and currently displayed in WebView, a VRML browser modified to support the Virtual Reality Behavior System (VRBS) protocol. VRBS provides communication between multiple client browsers, each capable of manipulating the scene. This level of collaboration works well over standard Internet connections and holds promise for collaborative research at a distance and distance learning. Further, via VRBS, the VRML world can be used as a visual cue to trigger an application such as a remote MEME search. MICE is very much work in progress. Current work seeks to replace WebView with Netscape, Cosmoplayer, a standard VRML plug-in, and a Java-based console. The console consists of a generic kernel suitable for multiple collaborative applications and additional application-specific controls. Further details of the MICE project are available at http:/(/)mice.sdsc.edu.

Computational Biology↗
PubMed1997

Code generation through annotation of macromolecular structure data.

The maintenance of software which uses a rapidly evolving data annotation scheme is time consuming and expensive. At the same time without current software the annotation scheme itself becomes limited and is less likely to be widely adopted. A solution to this problem has been developed for the macromolecular Crystallographic Information File (mmCIF) annotation scheme. The approach could be generalized for a variety of annotation schemes used or proposed for molecular biology data. mmCIF provides a highly structured and complete annotation for describing NMR and X-ray crystallographic data and the resulting macromolecular structures. This annotation is maintained in the mmCIF dictionary which currently contains over 3,200 terms. A major challenge is to maintain code for converting between mmCIF and Protein Data Bank (PDB) annotations while both continue to evolve. The solution has been to define a simple domain specific language (DSL) which is added to the extensive annotation already found in the mmCIF dictionary. The DSL calls specific mapping modules for each category of data item in the mmCIF dictionary. Adding or changing the mapping between PDB and mmCIF items of data is straightforward since data categories (and hence mapping modules) correspond to elements of macromolecular structure familiar to the experimentalist. Each time a change is made to the macromolecular annotation the appropriate change is made to the easily located and modifiable mapping modules. A code generator is then called which reads the mapping modules and creates a new executable for performing the data conversion. In this way code is easily kept current by individuals with limited programming skill, but who have an understanding of macromolecular structure and details of the annotation scheme. Most important, the conversion process becomes part of the global dictionary and is not open to a variety of interpretations by different research groups writing code based on dictionary contents. Details of the DSL and code generator are provided.

Crystallography, X-Ray↗
PubMed1993

Estrogen receptor analysis of human temporomandibular disc.

Epidemiological studies of temporomandibular joint (TMJ) dysfunction suggest a significant female predilection for symptomatic disease. Because previous primate research revealed sexual dimorphism in the estrogen receptors (ER) present in the masticatory apparatus, this investigation was undertaken to assess the presence of ER in human TMJ tissues. The negative findings suggest that ER status does not contribute to symptomatic TMJ disease.

Adolescent↗
PubMedDate not supplied

Engineering a human bone marrow model: a case study on ex vivo erythropoiesis.

Bone marrow, with its intricate, three-dimensional tissue structure facilitating cell-cell interactions, provides a microenvironment supporting the production of hundreds of billions of multilineal blood cells everyday. We have developed a three-dimensional bone marrow culture system in which marrow cells are cultured in a reactor packed with porous microspheres. The culture supports a three-dimensional growth configuration and multilineal hemopoiesis mimicking the bone marrow in vivo. We studied ex vivo human erythropoiesis using the three-dimensional culture system. The system sustained extensive erythropoiesis at low erythropoietin concentrations (0.2 U/mL), plus stem cell factor, interleukin-3, granulocyte-macrophage colony-stimulating factor, and insulin-like growth factor-I. Erythroid cell production lasted for more than 5 weeks, and the percentage of erythroid cells in the nonadherent cell population was approximately 60%. Flow cytometric analysis using cell surface markers specific for erythroid cells (CD71 and glycophorin-A) indicated that the culture produced early, intermediate, and late erythroid cells. As the culture progressed, the erythroid cell population shifted gradually toward mature cell types. When compared to the three-dimensional culture, the traditional flask cultures failed to support extensive erythropoiesis under the same conditions. This indicates that the three-dimensional bone marrow culture system provides a microenvironment conducive to erythropoiesis under more physiological conditions and is a better bone marrow model.

Biomedical Engineering↗
PubMedDate not supplied

[Likeness: a system for rapid retrieval of similar conformation of proteins and their spatial structures].

We report a method for estimating the conformational likeness between any two proteins. Likeness is handled in terms of stochastic geometry, fuzzy logic and decision making theories. Using the method, a computer system LIKENESS was developed. The system does "real time" searching and spatial alignment of any PDB-available proteins. LIKENESS is accessible at URL: "http:@cl.sdsc.edu/".

Amino Acid Sequence↗
PubMedDate not supplied

[WWWMGS: an integrated server for molecular-genetic studies].

We report an integrative technology for molecular biology studies in the field of transcription regulation by using Internet. A set of databases, programs, and systems are included into WWWMGS Web server. For example, the use of TRRD database information for site prediction is described. Using this method, the computer system SeqAnn was developed. The system performs the "real time" searching for prediction of initiation transcription site position according to database information. WWWMGS is available at URL: http://wwwmgs.bionet.nsc.ru/.

Base Sequence↗
PubMedDate not supplied

Differential diagnosis of malignant lymphomas by imprint cytology.

The results of a study of 214 touch imprints of benign and malignant lymphoid disorders are presented. The diagnostic criteria, including the results of special stains, are described for both benign proliferative disorders and malignant lymphomas. Imprint cytology achieved an accuracy of 99% in diagnosing both benign and malignant conditions. Specific subtyping of malignant disorders was correctly made in 83% of non-Hodgkin's lymphomas and in 66% of Hodgkin's lymphomas. It is concluded that imprint cytology is a useful adjunct to the histopathologic diagnosis of lymphoid disease.

Cytodiagnosis↗