Biomedical subjects

Steven P Bennett

Publications and source records attributed to Steven P Bennett.

3 recordsLinked to original sources

PubMed2005

Lymphopenia and spontaneous autorosette formation in SOD1 mouse model of ALS.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by motoneuron degeneration. Increasing evidence suggests immune system involvement in ALS pathogenesis but information about peripheral blood characteristics has been lacking. We evaluated hematological and morphological parameters in peripheral blood of G93A SOD1 mice. A significant decrease in white blood cells was found at the end stage of disease. The lymphocyte reduction may suggest immunodeficiency in ALS. Spontaneously forming rosettes with autologous erythrocytes were noted in approximately 28% of lymphocytes in SOD1 mice. To our knowledge, this is the first study characterizing hematology and revealing autorosettes in the SOD1 mouse model of ALS at the terminal phase of disease.

Amyotrophic Lateral Sclerosis↗

PubMed2003

3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs.

Computational methods such as sequence alignment and motif construction are useful in grouping related proteins into families, as well as helping to annotate new proteins of unknown function. These methods identify conserved amino acids in protein sequences, but cannot determine the specific functional or structural roles of conserved amino acids without additional study. In this work, we present 3MATRIX (http://3matrix.stanford.edu) and 3MOTIF (http://3motif.stanford.edu), a web-based sequence motif visualization system that displays sequence motif information in its appropriate three-dimensional (3D) context. This system is flexible in that users can enter sequences, keywords, structures or sequence motifs to generate visualizations. In 3MOTIF, users can search using discrete sequence motifs such as PROSITE patterns, eMOTIFs, or any other regular expression-like motif. Similarly, 3MATRIX accepts an eMATRIX position-specific scoring matrix, or will convert a multiple sequence alignment block into an eMATRIX for visualization. Each query motif is used to search the protein structure database for matches, in which the motif is then visually highlighted in three dimensions. Important properties of motifs such as sequence conservation and solvent accessible surface area are also displayed in the visualizations, using carefully chosen color shading schemes.

Amino Acid Motifs↗

PubMed2003

3MOTIF: visualizing conserved protein sequence motifs in the protein structure database.

SUMMARY: 3MOTIF is a web application that visually maps conserved sequence motifs onto three-dimensional protein structures in the Protein Data Bank (PDB; Berman et al., Nucleic Acids Res., 28, 235-242, 2000). Important properties of motifs such as conservation strength and solvent accessible surface area at each position are visually represented on the structure using a variety of color shading schemes. Users can manipulate the displayed motifs using the freely available Chime plugin. AVAILABILITY: http://motif.stanford.edu/3motif/

Amino Acid Motifs↗